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Omenn GS, Lane L, Overall CM, Lindskog C, Pineau C, Packer NH, Cristea IM, Weintraub ST, Orchard S, Roehrl MHA, Nice E, Guo T, Van Eyk JE, Liu S, Bandeira N, Aebersold R, Moritz RL, Deutsch EW. The 2023 Report on the Proteome from the HUPO Human Proteome Project. J Proteome Res 2024; 23:532-549. [PMID: 38232391 PMCID: PMC11026053 DOI: 10.1021/acs.jproteome.3c00591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Since 2010, the Human Proteome Project (HPP), the flagship initiative of the Human Proteome Organization (HUPO), has pursued two goals: (1) to credibly identify the protein parts list and (2) to make proteomics an integral part of multiomics studies of human health and disease. The HPP relies on international collaboration, data sharing, standardized reanalysis of MS data sets by PeptideAtlas and MassIVE-KB using HPP Guidelines for quality assurance, integration and curation of MS and non-MS protein data by neXtProt, plus extensive use of antibody profiling carried out by the Human Protein Atlas. According to the neXtProt release 2023-04-18, protein expression has now been credibly detected (PE1) for 18,397 of the 19,778 neXtProt predicted proteins coded in the human genome (93%). Of these PE1 proteins, 17,453 were detected with mass spectrometry (MS) in accordance with HPP Guidelines and 944 by a variety of non-MS methods. The number of neXtProt PE2, PE3, and PE4 missing proteins now stands at 1381. Achieving the unambiguous identification of 93% of predicted proteins encoded from across all chromosomes represents remarkable experimental progress on the Human Proteome parts list. Meanwhile, there are several categories of predicted proteins that have proved resistant to detection regardless of protein-based methods used. Additionally there are some PE1-4 proteins that probably should be reclassified to PE5, specifically 21 LINC entries and ∼30 HERV entries; these are being addressed in the present year. Applying proteomics in a wide array of biological and clinical studies ensures integration with other omics platforms as reported by the Biology and Disease-driven HPP teams and the antibody and pathology resource pillars. Current progress has positioned the HPP to transition to its Grand Challenge Project focused on determining the primary function(s) of every protein itself and in networks and pathways within the context of human health and disease.
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Affiliation(s)
- Gilbert S. Omenn
- University of Michigan, Ann Arbor, Michigan 48109, United States
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and University of Geneva, 1015 Lausanne, Switzerland
| | - Christopher M. Overall
- University of British Columbia, Vancouver, BC V6T 1Z4, Canada, Yonsei University Republic of Korea
| | | | - Charles Pineau
- University Rennes, Inserm U1085, Irset, 35042 Rennes, France
| | | | | | - Susan T. Weintraub
- University of Texas Health Science Center-San Antonio, San Antonio, Texas 78229-3900, United States
| | | | - Michael H. A. Roehrl
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, United States
| | | | - Tiannan Guo
- Westlake Center for Intelligent Proteomics, Westlake Laboratory, Westlake University, Hangzhou 310024, Zhejiang Province, China
| | - Jennifer E. Van Eyk
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, 127 South San Vicente Boulevard, Pavilion, 9th Floor, Los Angeles, CA, 90048, United States
| | - Siqi Liu
- BGI Group, Shenzhen 518083, China
| | - Nuno Bandeira
- University of California, San Diego, La Jolla, CA, 92093, United States
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology in ETH Zurich, 8092 Zurich, Switzerland
- University of Zurich, 8092 Zurich, Switzerland
| | - Robert L. Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Eric W. Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
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2
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Zuffa S, Schmid R, Bauermeister A, P Gomes PW, Caraballo-Rodriguez AM, El Abiead Y, Aron AT, Gentry EC, Zemlin J, Meehan MJ, Avalon NE, Cichewicz RH, Buzun E, Terrazas MC, Hsu CY, Oles R, Ayala AV, Zhao J, Chu H, Kuijpers MCM, Jackrel SL, Tugizimana F, Nephali LP, Dubery IA, Madala NE, Moreira EA, Costa-Lotufo LV, Lopes NP, Rezende-Teixeira P, Jimenez PC, Rimal B, Patterson AD, Traxler MF, Pessotti RDC, Alvarado-Villalobos D, Tamayo-Castillo G, Chaverri P, Escudero-Leyva E, Quiros-Guerrero LM, Bory AJ, Joubert J, Rutz A, Wolfender JL, Allard PM, Sichert A, Pontrelli S, Pullman BS, Bandeira N, Gerwick WH, Gindro K, Massana-Codina J, Wagner BC, Forchhammer K, Petras D, Aiosa N, Garg N, Liebeke M, Bourceau P, Kang KB, Gadhavi H, de Carvalho LPS, Silva Dos Santos M, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, Vera Ponce de León A, Pope PB, La Rosa SL, La Barbera G, Roager HM, Laursen MF, Hammerle F, Siewert B, Peintner U, Licona-Cassani C, Rodriguez-Orduña L, Rampler E, Hildebrand F, Koellensperger G, Schoeny H, Hohenwallner K, Panzenboeck L, Gregor R, O'Neill EC, Roxborough ET, Odoi J, Bale NJ, Ding S, Sinninghe Damsté JS, Guan XL, Cui JJ, Ju KS, Silva DB, Silva FMR, da Silva GF, Koolen HHF, Grundmann C, Clement JA, Mohimani H, Broders K, McPhail KL, Ober-Singleton SE, Rath CM, McDonald D, Knight R, Wang M, Dorrestein PC. microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data. Nat Microbiol 2024; 9:336-345. [PMID: 38316926 PMCID: PMC10847041 DOI: 10.1038/s41564-023-01575-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/29/2023] [Indexed: 02/07/2024]
Abstract
microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbe-derived metabolites and relative producers without a priori knowledge will vastly enhance the understanding of microorganisms' role in ecology and human health.
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Affiliation(s)
- Simone Zuffa
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Robin Schmid
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Anelize Bauermeister
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paulo Wender P Gomes
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Andres M Caraballo-Rodriguez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Yasin El Abiead
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Allegra T Aron
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA
| | - Emily C Gentry
- Department of Chemistry, Virginia Tech, Blacksburg, VA, USA
| | - Jasmine Zemlin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA, USA
| | - Michael J Meehan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Nicole E Avalon
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Robert H Cichewicz
- Department of Chemistry and Biochemistry, College of Arts and Sciences, University of Oklahoma, Norman, OK, USA
| | - Ekaterina Buzun
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Marvic Carrillo Terrazas
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Chia-Yun Hsu
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Renee Oles
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Adriana Vasquez Ayala
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Jiaqi Zhao
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Hiutung Chu
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
- Center for Mucosal Immunology, Allergy, and Vaccines (cMAV), Chiba University-University of California San Diego, San Diego, CA, USA
| | - Mirte C M Kuijpers
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, San Diego, CA, USA
| | - Sara L Jackrel
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, San Diego, CA, USA
| | - Fidele Tugizimana
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa
- International Research and Development, Omnia Nutriology, Omnia Group (Pty) Ltd, Johannesburg, South Africa
| | - Lerato Pertunia Nephali
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa
| | - Ian A Dubery
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa
| | - Ntakadzeni Edwin Madala
- Department of Biochemistry and Microbiology, Faculty of Sciences, Agriculture and Engineering, University of Venda, Thohoyandou, South Africa
| | - Eduarda Antunes Moreira
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Leticia Veras Costa-Lotufo
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Norberto Peporine Lopes
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Paula Rezende-Teixeira
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paula C Jimenez
- Department of Marine Science, Institute of Marine Science, Federal University of São Paulo, Santos, Brazil
| | - Bipin Rimal
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Matthew F Traxler
- Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, Berkeley, CA, USA
| | - Rita de Cassia Pessotti
- Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, Berkeley, CA, USA
| | - Daniel Alvarado-Villalobos
- Metabolomics and Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
| | - Giselle Tamayo-Castillo
- Metabolomics and Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
- Escuela de Química, Universidad de Costa Rica, San José, Costa Rica
| | - Priscila Chaverri
- Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA) and Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
- Department of Natural Sciences, Bowie State University, Bowie, MD, USA
| | - Efrain Escudero-Leyva
- Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
| | - Luis-Manuel Quiros-Guerrero
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Alexandre Jean Bory
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Juliette Joubert
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Adriano Rutz
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Andreas Sichert
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Sammy Pontrelli
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Benjamin S Pullman
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - William H Gerwick
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Katia Gindro
- Plant Protection, Mycology group, Agroscope, Nyon, Switzerland
| | | | - Berenike C Wagner
- Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Karl Forchhammer
- Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Daniel Petras
- Cluster of Excellence 'Controlling Microbes to Fight Infections' (CMFI), University of Tuebingen, Tuebingen, Germany
| | - Nicole Aiosa
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Manuel Liebeke
- Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Bremen, Germany
- Department for Metabolomics, Kiel University, Kiel, Germany
| | - Patric Bourceau
- Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Kyo Bin Kang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, Korea
| | - Henna Gadhavi
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK
- King's College London, London, UK
| | - Luiz Pedro Sorio de Carvalho
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK
- Chemistry Department, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, USA
| | | | - Alicia Isabel Pérez-Lorente
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Malaga, Spain
| | - Carlos Molina-Santiago
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Malaga, Spain
| | - Diego Romero
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Malaga, Spain
| | - Raimo Franke
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Braunschweig, Germany
| | - Arturo Vera Ponce de León
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Phillip Byron Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Sabina Leanti La Rosa
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Giorgia La Barbera
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Henrik M Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | | | - Fabian Hammerle
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Bianka Siewert
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Ursula Peintner
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Cuauhtemoc Licona-Cassani
- Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Monterrey, Mexico
| | - Lorena Rodriguez-Orduña
- Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Monterrey, Mexico
| | - Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Felina Hildebrand
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Harald Schoeny
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Katharina Hohenwallner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Lisa Panzenboeck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Rachel Gregor
- Department of Civil and Environmental Engineering, School of Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | - Jane Odoi
- Faculty of Engineering, University of Nottingham, Nottingham, UK
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands
| | - Su Ding
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands
| | - Xue Li Guan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Jerry J Cui
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, USA
| | - Kou-San Ju
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, USA
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA
| | - Denise Brentan Silva
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Fernanda Motta Ribeiro Silva
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Hector H F Koolen
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Carlismari Grundmann
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | | | - Hosein Mohimani
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kirk Broders
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL, USA
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Sidnee E Ober-Singleton
- Department of Physics, Study of Heavy-Element-Biomaterials, University of Oregon, Eugene, OR, USA
| | | | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Rob Knight
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
| | - Mingxun Wang
- Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
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3
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Zuffa S, Schmid R, Bauermeister A, Gomes PWP, Caraballo-Rodriguez AM, Abiead YE, Aron AT, Gentry EC, Zemlin J, Meehan MJ, Avalon NE, Cichewicz RH, Buzun E, Terrazas MC, Hsu CY, Oles R, Ayala AV, Zhao J, Chu H, Kuijpers MCM, Jackrel SL, Tugizimana F, Nephali LP, Dubery IA, Madala NE, Moreira EA, Costa-Lotufo LV, Lopes NP, Rezende-Teixeira P, Jimenez PC, Rimal B, Patterson AD, Traxler MF, de Cassia Pessotti R, Alvarado-Villalobos D, Tamayo-Castillo G, Chaverri P, Escudero-Leyva E, Quiros-Guerrero LM, Bory AJ, Joubert J, Rutz A, Wolfender JL, Allard PM, Sichert A, Pontrelli S, Pullman BS, Bandeira N, Gerwick WH, Gindro K, Massana-Codina J, Wagner BC, Forchhammer K, Petras D, Aiosa N, Garg N, Liebeke M, Bourceau P, Kang KB, Gadhavi H, de Carvalho LPS, dos Santos MS, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, de León AVP, Pope PB, Rosa SLL, Barbera GL, Roager HM, Laursen MF, Hammerle F, Siewert B, Peintner U, Licona-Cassani C, Rodriguez-Orduña L, Rampler E, Hildebrand F, Koellensperger G, Schoeny H, Hohenwallner K, Panzenboeck L, Gregor R, O’Neill EC, Roxborough ET, Odoi J, Bale NJ, Ding S, Sinninghe Damsté JS, Guan XL, Cui JJ, Ju KS, Silva DB, Silva FMR, da Silva GF, Koolen HHF, Grundmann C, Clement JA, Mohimani H, Broders K, McPhail KL, Ober-Singleton SE, Rath CM, McDonald D, Knight R, Wang M, Dorrestein PC. A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data. Res Sq 2023:rs.3.rs-3189768. [PMID: 37577622 PMCID: PMC10418563 DOI: 10.21203/rs.3.rs-3189768/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, without a priori knowledge, will vastly enhance the understanding of microorganisms' role in ecology and human health.
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Affiliation(s)
- Simone Zuffa
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Robin Schmid
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Anelize Bauermeister
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, Av. Lineu Prestes 1524, São Paulo, SP, 05508-000, Brazil
| | - Paulo Wender P. Gomes
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Andres M. Caraballo-Rodriguez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Yasin El Abiead
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Allegra T. Aron
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80210, United States
| | - Emily C. Gentry
- Department of Chemistry, Virginia Tech, Blacksburg, VA, 24061, United States
| | - Jasmine Zemlin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Center for Microbiome Innovation, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Michael J. Meehan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Nicole E. Avalon
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, United States
| | - Robert H. Cichewicz
- Department of Chemistry and Biochemistry, College of Arts and Sciences, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, United States
| | - Ekaterina Buzun
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Marvic Carrillo Terrazas
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Chia-Yun Hsu
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Renee Oles
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Adriana Vasquez Ayala
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Jiaqi Zhao
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Hiutung Chu
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Center for Mucosal Immunology, Allergy, and Vaccines (cMAV), Chiba University-University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Mirte C. M. Kuijpers
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Sara L. Jackrel
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Fidele Tugizimana
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Auckland Park, Johannesburg, Gauteng, 2006, South Africa
- International Research and Development, Omnia Nutriology, Omnia Group (Pty) Ltd, 178 Montecasino Boulevard, Fourways, Johannesburg, Gauteng, 2191, South Africa
| | - Lerato Pertunia Nephali
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Auckland Park, Johannesburg, Gauteng, 2006, South Africa
| | - Ian A. Dubery
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Auckland Park, Johannesburg, Gauteng, 2006, South Africa
| | - Ntakadzeni Edwin Madala
- Department of Biochemistry and Microbiology, Faculty of Sciences, Agriculture and Engineering, University of Venda, Private Bag X5050, Thohoyandou, Limpopo, 950, South Africa
| | - Eduarda Antunes Moreira
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida do Café, Ribeirão Preto, SP, 14040-903, Brazil
| | - Leticia Veras Costa-Lotufo
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, Av. Lineu Prestes 1524, São Paulo, SP, 05508-000, Brazil
| | - Norberto Peporine Lopes
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida do Café, Ribeirão Preto, SP, 14040-903, Brazil
| | - Paula Rezende-Teixeira
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, Av. Lineu Prestes 1524, São Paulo, SP, 05508-000, Brazil
| | - Paula C. Jimenez
- Department of Marine Science, Institute of Marine Science, Federal University of São Paulo, Rua Carvalho de Mendonça, 144, Santos, SP, 11070-100, Brazil
| | - Bipin Rimal
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, 319 Life Sciences Building, University Park, PA, 16802, United States
| | - Andrew D. Patterson
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, 320 Life Sciences Building, University Park, PA, 16802, United States
| | - Matthew F. Traxler
- Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, 311 Koshland Hall, Berkeley, CA, 94270, United States
| | - Rita de Cassia Pessotti
- Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, 311 Koshland Hall, Berkeley, CA, 94270, United States
| | - Daniel Alvarado-Villalobos
- Metabolomics & Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
| | - Giselle Tamayo-Castillo
- Metabolomics & Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
- Escuela de Química, Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
| | - Priscila Chaverri
- Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA) & Escuela de Biología, Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
- Department of Natural Sciences, Bowie State University, Bowie, Maryland, 20715, United States
| | - Efrain Escudero-Leyva
- Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
| | - Luis-Manuel Quiros-Guerrero
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
| | - Alexandre Jean Bory
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
| | - Juliette Joubert
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
| | - Adriano Rutz
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, Zürich, 8093, Switzerland
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Department of Biology, University of Fribourg, Chemin du Musée, 10, Fribourg, FR, 1700, Switzerland
| | - Andreas Sichert
- Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, Zürich, 8093, Switzerland
| | - Sammy Pontrelli
- Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, Zürich, 8093, Switzerland
| | - Benjamin S Pullman
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - William H. Gerwick
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Katia Gindro
- Plant Protection, Mycology group, Agroscope, Rte de Duillier, 50, Nyon, VD, 1260, Switzerland
| | - Josep Massana-Codina
- Plant Protection, Mycology group, Agroscope, Rte de Duillier, 50, Nyon, VD, 1260, Switzerland
| | - Berenike C. Wagner
- Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Auf der Morgenstelle 28, Tuebingen, 72076, Germany
| | - Karl Forchhammer
- Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Auf der Morgenstelle 28, Tuebingen, 72076, Germany
| | - Daniel Petras
- Cluster of Excellence “Controlling Microbes to Fight Infections” (CMFI), University of Tuebingen, Auf der Morgenstelle 24, Tuebingen, 72076, Germany
| | - Nicole Aiosa
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA, 30332, United States
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA, 30332, United States
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA, 30332, United States
| | - Manuel Liebeke
- Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, 28359, Germany
| | - Patric Bourceau
- Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, 28359, Germany
| | - Kyo Bin Kang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women’s University, Cheongpa-ro 47 gil 100, Seoul, 04310, Korea
| | - Henna Gadhavi
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- King’s College London, Strand, London, WC2R 2LS, UK
| | - Luiz Pedro Sorio de Carvalho
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Chemistry Department, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 110 Scripps Way, Jupiter, FL, 33458, United States
| | - Mariana Silva dos Santos
- Metabolomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Alicia Isabel Pérez-Lorente
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea ‘‘La Mayora’’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Málaga, Málaga, 29071, Spain
| | - Carlos Molina-Santiago
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea ‘‘La Mayora’’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Málaga, Málaga, 29071, Spain
| | - Diego Romero
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea ‘‘La Mayora’’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Málaga, Málaga, 29071, Spain
| | - Raimo Franke
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, 38124, Germany
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, 38124, Germany
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Braunschweig, 38124, Germany
| | - Arturo Vera Ponce de León
- Faculty of Chemistry, BIotechnology and Food Science, Norwegian University of Life Sciences, Postboks 5003, Ås, 1433, Norway
| | - Phillip Byron Pope
- Faculty of Chemistry, BIotechnology and Food Science, Norwegian University of Life Sciences, Postboks 5003, Ås, 1433, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Postboks 5003, Ås, 1433, Norway
| | - Sabina Leanti La Rosa
- Faculty of Chemistry, BIotechnology and Food Science, Norwegian University of Life Sciences, Postboks 5003, Ås, 1433, Norway
| | - Giorgia La Barbera
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Rolighedsvej 26, Frederiksberg, 1958, Denmark
| | - Henrik M. Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Rolighedsvej 26, Frederiksberg, 1958, Denmark
| | - Martin Frederik Laursen
- National Food Institute, Technical University of Denmark, Kemitorvet B202, Lyngby, 2800, Denmark
| | - Fabian Hammerle
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innrain 80-82, Innsbruck, 6020, Austria
| | - Bianka Siewert
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innrain 80-82, Innsbruck, 6020, Austria
| | - Ursula Peintner
- Department of Microbiology, University of Innsbruck, Technikerstr. 25, Innsbruck, 6020, Austria
| | - Cuauhtemoc Licona-Cassani
- Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501, Monterrey, Nuevo Leon, 64849, Mexico
| | - Lorena Rodriguez-Orduña
- Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501, Monterrey, Nuevo Leon, 64849, Mexico
| | - Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
| | - Felina Hildebrand
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Waehringer Str. 42, Vienna, 1090, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstr. 14,, Vienna, 1090, Austria
| | - Harald Schoeny
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
| | - Katharina Hohenwallner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Waehringer Str. 42, Vienna, 1090, Austria
| | - Lisa Panzenboeck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Waehringer Str. 42, Vienna, 1090, Austria
| | - Rachel Gregor
- Department of Civil and Environmental Engineering, School of Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02142, United States
| | - Ellis Charles O’Neill
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG72RD, UK
| | | | - Jane Odoi
- Faculty of Engineering, University of Nottingham, University Park, Nottingham, NG72RD, UK
| | - Nicole J. Bale
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), Landsdiep 4, t Horntje (Texel), 1797 SZ, Netherlands
| | - Su Ding
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), Landsdiep 4, t Horntje (Texel), 1797 SZ, Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), Landsdiep 4, t Horntje (Texel), 1797 SZ, Netherlands
| | - Xueli Li Guan
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, Singapore, 636921, Singapore
| | - Jerry J. Cui
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States
| | - Kou-San Ju
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States
- Center for Applied Plant Sciences, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States
- Infectious Diseases Institute, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States
| | - Denise Brentan Silva
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Av. Costa e Silva, s/n, Campo Grande, MS, 79070-900, Brazil
| | - Fernanda Motta Ribeiro Silva
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Av. Costa e Silva, s/n, Campo Grande, MS, 79070-900, Brazil
| | | | - Hector H. F. Koolen
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, 1777 Carvalho Leal Avenue, Manaus, AM, 69065-001, Brazil
| | - Carlismari Grundmann
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida do Café, Ribeirão Preto, SP, 14040-903, Brazil
| | - Jason A. Clement
- Baruch S. Blumberg Institute, 3805 Old Easton Rd., Doylestown, PA, 18902, United States
| | - Hosein Mohimani
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, United States
| | - Kirk Broders
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N. University, Peoria, IL, 61604, United States
| | - Kerry L. McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Weniger Hall, room 341, Corvallis, OR, 97331, United States
| | - Sidnee E. Ober-Singleton
- Department of Physics, Study of Heavy-Element-Biomaterials, University of Oregon, 1255 E 13th Ave, Basement, Eugene, OR, 97402, United States
| | | | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Rob Knight
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Department of Pediatrics, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Mingxun Wang
- Department of Computer Science and Engineering, University of California Riverside, 900 University Ave., Riverside, CA, 92521, United States
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
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4
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Deutsch EW, Vizcaíno JA, Jones AR, Binz PA, Lam H, Klein J, Bittremieux W, Perez-Riverol Y, Tabb DL, Walzer M, Ricard-Blum S, Hermjakob H, Neumann S, Mak TD, Kawano S, Mendoza L, Van Den Bossche T, Gabriels R, Bandeira N, Carver J, Pullman B, Sun Z, Hoffmann N, Shofstahl J, Zhu Y, Licata L, Quaglia F, Tosatto SCE, Orchard SE. Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. J Proteome Res 2023; 22:287-301. [PMID: 36626722 PMCID: PMC9903322 DOI: 10.1021/acs.jproteome.2c00637] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Indexed: 01/11/2023]
Abstract
The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been successfully developing guidelines, data formats, and controlled vocabularies (CVs) for the proteomics community and other fields supported by mass spectrometry since its inception 20 years ago. Here we describe the general operation of the PSI, including its leadership, working groups, yearly workshops, and the document process by which proposals are thoroughly and publicly reviewed in order to be ratified as PSI standards. We briefly describe the current state of the many existing PSI standards, some of which remain the same as when originally developed, some of which have undergone subsequent revisions, and some of which have become obsolete. Then the set of proposals currently being developed are described, with an open call to the community for participation in the forging of the next generation of standards. Finally, we describe some synergies and collaborations with other organizations and look to the future in how the PSI will continue to promote the open sharing of data and thus accelerate the progress of the field of proteomics.
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Affiliation(s)
- Eric W. Deutsch
- Institute
for Systems Biology, Seattle, Washington 98109, United States
| | - Juan Antonio Vizcaíno
- European
Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Andrew R. Jones
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Pierre-Alain Binz
- Clinical
Chemistry Service, Lausanne University Hospital, 1011 976 Lausanne, Switzerland
| | - Henry Lam
- Department
of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, P. R. China.
| | - Joshua Klein
- Program for
Bioinformatics, Boston University, Boston, Massachusetts 02215, United States
| | - Wout Bittremieux
- Skaggs
School
of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
- Department
of Computer Science, University of Antwerp, 2020 Antwerpen, Belgium
| | - Yasset Perez-Riverol
- European
Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - David L. Tabb
- SA MRC
Centre for TB Research, DST/NRF Centre of Excellence for Biomedical
TB Research, Division of Molecular Biology and Human Genetics, Faculty
of Medicine and Health Sciences, Stellenbosch
University, Cape Town 7602, South Africa
| | - Mathias Walzer
- European
Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Sylvie Ricard-Blum
- Univ.
Lyon, Université Lyon 1, ICBMS, UMR 5246, 69622 Villeurbanne, France
| | - Henning Hermjakob
- European
Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Steffen Neumann
- Bioinformatics
and Scientific Data, Leibniz Institute of
Plant Biochemistry, 06120 Halle, Germany
- German
Centre for Integrative Biodiversity Research (iDiv), 04103 Halle-Jena-Leipzig, Germany
| | - Tytus D. Mak
- Mass Spectrometry
Data Center, National Institute of Standards
and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United
States
| | - Shin Kawano
- Database
Center for Life Science, Joint Support Center for Data Science Research, Research Organization of Information and Systems, Chiba 277-0871, Japan
- Faculty
of Contemporary Society, Toyama University
of International Studies, Toyama 930-1292, Japan
- School
of Frontier Engineering, Kitasato University, Sagamihara 252-0373, Japan
| | - Luis Mendoza
- Institute
for Systems Biology, Seattle, Washington 98109, United States
| | - Tim Van Den Bossche
- VIB-UGent
Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
- Department
of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052 Ghent, Belgium
| | - Ralf Gabriels
- VIB-UGent
Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
- Department
of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052 Ghent, Belgium
| | - Nuno Bandeira
- Skaggs
School
of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
- Center
for Computational Mass Spectrometry, Department of Computer Science
and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego 92093-0404, United States
| | - Jeremy Carver
- Center
for Computational Mass Spectrometry, Department of Computer Science
and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego 92093-0404, United States
| | - Benjamin Pullman
- Center
for Computational Mass Spectrometry, Department of Computer Science
and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego 92093-0404, United States
| | - Zhi Sun
- Institute
for Systems Biology, Seattle, Washington 98109, United States
| | - Nils Hoffmann
- Institute
for Bio- and Geosciences (IBG-5), Forschungszentrum
Jülich GmbH, 52428 Jülich, Germany
| | - Jim Shofstahl
- Thermo
Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Yunping Zhu
- National
Center for Protein Sciences (Beijing), Beijing
Institute of Lifeomics, #38, Life Science Park, Changping District, Beijing 102206, China
| | - Luana Licata
- Fondazione
Human Technopole, 20157 Milan, Italy
- Department
of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Federica Quaglia
- Institute
of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR-IBIOM), 70126 Bari, Italy
- Department
of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | | | - Sandra E. Orchard
- European
Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
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5
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Deutsch EW, Bandeira N, Perez-Riverol Y, Sharma V, Carver J, Mendoza L, Kundu DJ, Wang S, Bandla C, Kamatchinathan S, Hewapathirana S, Pullman B, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, MacLean B, MacCoss M, Zhu Y, Ishihama Y, Vizcaíno J. The ProteomeXchange consortium at 10 years: 2023 update. Nucleic Acids Res 2023; 51:D1539-D1548. [PMID: 36370099 PMCID: PMC9825490 DOI: 10.1093/nar/gkac1040] [Citation(s) in RCA: 126] [Impact Index Per Article: 126.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/20/2022] [Accepted: 10/23/2022] [Indexed: 11/13/2022] Open
Abstract
Mass spectrometry (MS) is by far the most used experimental approach in high-throughput proteomics. The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) was originally set up to standardize data submission and dissemination of public MS proteomics data. It is now 10 years since the initial data workflow was implemented. In this manuscript, we describe the main developments in PX since the previous update manuscript in Nucleic Acids Research was published in 2020. The six members of the Consortium are PRIDE, PeptideAtlas (including PASSEL), MassIVE, jPOST, iProX and Panorama Public. We report the current data submission statistics, showcasing that the number of datasets submitted to PX resources has continued to increase every year. As of June 2022, more than 34 233 datasets had been submitted to PX resources, and from those, 20 062 (58.6%) just in the last three years. We also report the development of the Universal Spectrum Identifiers and the improvements in capturing the experimental metadata annotations. In parallel, we highlight that data re-use activities of public datasets continue to increase, enabling connections between PX resources and other popular bioinformatics resources, novel research and also new data resources. Finally, we summarise the current state-of-the-art in data management practices for sensitive human (clinical) proteomics data.
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Affiliation(s)
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Dept. Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Jeremy J Carver
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Dept. Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Luis Mendoza
- Institute for Systems Biology, Seattle WA 98109, USA
| | - Deepti J Kundu
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Shengbo Wang
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Chakradhar Bandla
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Selvakumar Kamatchinathan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Suresh Hewapathirana
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Benjamin S Pullman
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Dept. Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Julie Wertz
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Dept. Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Zhi Sun
- Institute for Systems Biology, Seattle WA 98109, USA
| | - Shin Kawano
- Faculty of Contemporary Society, Toyama University of International Studies, Toyama 930-1292, Japan
- Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Chiba 277-0871, Japan
- School of Frontier Engineering, Kitasato University, Sagamihara 252-0373, Japan
| | - Shujiro Okuda
- Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Yu Watanabe
- Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | | | | | - Yunping Zhu
- Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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6
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Leão TF, Wang M, da Silva R, Gurevich A, Bauermeister A, Gomes PWP, Brejnrod A, Glukhov E, Aron AT, Louwen JJR, Kim HW, Reher R, Fiore MF, van der Hooft JJJ, Gerwick L, Gerwick WH, Bandeira N, Dorrestein PC. NPOmix: A machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters. PNAS Nexus 2022; 1:pgac257. [PMID: 36712343 PMCID: PMC9802219 DOI: 10.1093/pnasnexus/pgac257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/18/2022] [Accepted: 11/25/2022] [Indexed: 06/02/2023]
Abstract
Microbial specialized metabolites are an important source of and inspiration for many pharmaceuticals, biotechnological products and play key roles in ecological processes. Untargeted metabolomics using liquid chromatography coupled with tandem mass spectrometry is an efficient technique to access metabolites from fractions and even environmental crude extracts. Nevertheless, metabolomics is limited in predicting structures or bioactivities for cryptic metabolites. Efficiently linking the biosynthetic potential inferred from (meta)genomics to the specialized metabolome would accelerate drug discovery programs by allowing metabolomics to make use of genetic predictions. Here, we present a k-nearest neighbor classifier to systematically connect mass spectrometry fragmentation spectra to their corresponding biosynthetic gene clusters (independent of their chemical class). Our new pattern-based genome mining pipeline links biosynthetic genes to metabolites that they encode for, as detected via mass spectrometry from bacterial cultures or environmental microbiomes. Using paired datasets that include validated genes-mass spectral links from the Paired Omics Data Platform, we demonstrate this approach by automatically linking 18 previously known mass spectra (17 for which the biosynthesis gene clusters can be found at the MIBiG database plus palmyramide A) to their corresponding previously experimentally validated biosynthetic genes (e.g., via nuclear magnetic resonance or genetic engineering). We illustrated a computational example of how to use our Natural Products Mixed Omics (NPOmix) tool for siderophore mining that can be reproduced by the users. We conclude that NPOmix minimizes the need for culturing (it worked well on microbiomes) and facilitates specialized metabolite prioritization based on integrative omics mining.
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Affiliation(s)
- Tiago F Leão
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba 13400-970, SP, Brazil
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Center for Computational Mass Spectrometry, University of California San Diego, La Jolla, CA 92093, USA
| | - Ricardo da Silva
- NPPNS, Physic and Chemistry Department, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-900, Brazil
| | - Alexey Gurevich
- Center for Algorithmic Biotechnology, St. Petersburg State University, St Petersburg 199004, Russia
| | - Anelize Bauermeister
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Paulo Wender P Gomes
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Asker Brejnrod
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Allegra T Aron
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Joris J R Louwen
- Bioinformatics Group, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Hyun Woo Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, Gyeonggi-do 10326, Korea
| | - Raphael Reher
- Institute of Pharmaceutical Biology and Biotechnology, University of Marburg, 35043 Marburg, Germany
| | - Marli F Fiore
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba 13400-970, SP, Brazil
| | | | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - William H Gerwick
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Nuno Bandeira
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Center for Computational Mass Spectrometry, University of California San Diego, La Jolla, CA 92093, USA
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7
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Omenn GS, Lane L, Overall CM, Pineau C, Packer NH, Cristea IM, Lindskog C, Weintraub ST, Orchard S, Roehrl MHA, Nice E, Liu S, Bandeira N, Chen YJ, Guo T, Aebersold R, Moritz RL, Deutsch EW. The 2022 Report on the Human Proteome from the HUPO Human Proteome Project. J Proteome Res 2022; 22:1024-1042. [PMID: 36318223 PMCID: PMC10081950 DOI: 10.1021/acs.jproteome.2c00498] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The 2022 Metrics of the Human Proteome from the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 407 (93.2%) of the 19 750 predicted proteins coded in the human genome, a net gain of 50 since 2021 from data sets generated around the world and reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 78 from 1421 to 1343. This represents continuing experimental progress on the human proteome parts list across all the chromosomes, as well as significant reclassifications. Meanwhile, applying proteomics in a vast array of biological and clinical studies continues to yield significant findings and growing integration with other omics platforms. We present highlights from the Chromosome-Centric HPP, Biology and Disease-driven HPP, and HPP Resource Pillars, compare features of mass spectrometry and Olink and Somalogic platforms, note the emergence of translation products from ribosome profiling of small open reading frames, and discuss the launch of the initial HPP Grand Challenge Project, "A Function for Each Protein".
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Affiliation(s)
- Gilbert S Omenn
- University of Michigan, Ann Arbor, Michigan48109, United States.,Institute for Systems Biology, Seattle, Washington98109, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and University of Geneva, 1015Lausanne, Switzerland
| | | | - Charles Pineau
- French Institute of Health and Medical Research, 35042RENNESCedexFrance
| | - Nicolle H Packer
- Macquarie University, Sydney, New South Wales2109, Australia.,Griffith University's Institute for Glycomics, Sydney, New South Wales2109, Australia
| | | | | | - Susan T Weintraub
- University of Texas Health Science Center-San Antonio, San Antonio, Texas78229-3900, United States
| | - Sandra Orchard
- EMBL-EBI, Hinxton, CambridgeshireCB10 1SD, United Kingdom
| | - Michael H A Roehrl
- Memorial Sloan Kettering Cancer Center, New York, New York10065, United States
| | - Edouard Nice
- Monash University, ClaytonVictoria3800, Australia
| | - Siqi Liu
- BGI Group, Shenzhen518083, P. R. China
| | - Nuno Bandeira
- University of California, San Diego, La Jolla, California92093, United States
| | - Yu-Ju Chen
- National Taiwan University, Academia Sinica, Nankang, Taipei11529, Taiwan
| | - Tiannan Guo
- Westlake University Guomics Laboratory of Big Proteomic Data, Hangzhou310024, ZhejiangProvinceP. R. China
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology in ETH Zurich, 8092Zurich, Switzerland
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington98109, United States
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington98109, United States
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8
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LeDuc RD, Deutsch EW, Binz PA, Fellers RT, Cesnik AJ, Klein JA, Van Den Bossche T, Gabriels R, Yalavarthi A, Perez-Riverol Y, Carver J, Bittremieux W, Kawano S, Pullman B, Bandeira N, Kelleher NL, Thomas PM, Vizcaíno JA. Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms. J Proteome Res 2022; 21:1189-1195. [PMID: 35290070 PMCID: PMC7612572 DOI: 10.1021/acs.jproteome.1c00771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
It is important for the proteomics community to have a standardized manner to represent all possible variations of a protein or peptide primary sequence, including natural, chemically-induced and artifactual modifications. The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) in collaboration with several members of the Consortium for Top-Down Proteomics (CTDP) has developed a standard notation called ProForma 2.0, which is a substantial extension of the original ProForma notation developed by the CTDP. ProForma 2.0 aims to unify the representation of proteoforms and peptidoforms. ProForma 2.0 supports use cases needed for bottom-up and middle-/top-down proteomics approaches and allows the encoding of highly modified proteins and peptides using a human-and machine-readable string. ProForma 2.0 can be used to represent protein modifications in a specified or ambiguous location, designated by mass shifts, chemical formulas, or controlled vocabulary terms, including cross-links (natural and chemical), and atomic isotopes. Notational conventions are based on public controlled vocabularies and ontologies. The most up-to-date full specification document and information about software implementations are available at http://psidev.info/proforma.
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Affiliation(s)
- Richard D LeDuc
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60611, United States
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Pierre-Alain Binz
- Clinical Chemistry Service, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Ryan T Fellers
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60611, United States
| | - Anthony J Cesnik
- Department of Genetics, Stanford University, Stanford, California 94305, United States.,Chan Zuckerberg Biohub, 499 Illinois Street, San Francisco, California 94158, United States.,SciLifeLab, School of Engineering Sciences in Chemistry Biotechnology and Health, KTH-Royal Institute of Technology, SE-171 21 Solna, Stockholm, Sweden 113 51
| | - Joshua A Klein
- Program for Bioinformatics, Boston University, Boston, Massachusetts 02215, United States
| | - Tim Van Den Bossche
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark 75-FSVM II, 9052 Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Ralf Gabriels
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark 75-FSVM II, 9052 Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Arshika Yalavarthi
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60611, United States
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, United Kingdom
| | | | | | - Shin Kawano
- Toyama University of International Studies, Toyama, 930-1292 Toyama, Higashikuromaki, 6 5-1, Japan.,Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Kashiwa, Chiba 277-0871, Japan
| | | | | | - Neil L Kelleher
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60611, United States
| | - Paul M Thomas
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60611, United States
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, United Kingdom
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9
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Oliveira S, Bandeira N, Leal JP, Maria L, Carretas JM, Monteiro B, Marçalo J. A new krypton complex – Experimental and computational investigation of the krypton sulphur pentafluoride cation, [KrSF 5] +, in the gas phase. Phys Chem Chem Phys 2022; 24:14631-14639. [DOI: 10.1039/d1cp05814b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The gas-phase reactions of noble gas (Ng) cations, namely Kr+ and Xe+, with SF6 were investigated experimentally by Fourier transform ion cyclotron resonance mass spectrometry and computationally using MP2 and...
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10
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Petras D, Phelan VV, Acharya D, Allen AE, Aron AT, Bandeira N, Bowen BP, Belle-Oudry D, Boecker S, Cummings DA, Deutsch JM, Fahy E, Garg N, Gregor R, Handelsman J, Navarro-Hoyos M, Jarmusch AK, Jarmusch SA, Louie K, Maloney KN, Marty MT, Meijler MM, Mizrahi I, Neve RL, Northen TR, Molina-Santiago C, Panitchpakdi M, Pullman B, Puri AW, Schmid R, Subramaniam S, Thukral M, Vasquez-Castro F, Dorrestein PC, Wang M. GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser. Nat Methods 2021; 19:134-136. [PMID: 34862502 DOI: 10.1038/s41592-021-01339-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Medicine, University of Tübingen, Tübingen, Germany
| | - Vanessa V Phelan
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Deepa Acharya
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Andrew E Allen
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
| | - Allegra T Aron
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Benjamin P Bowen
- DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Deirdre Belle-Oudry
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Simon Boecker
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Dale A Cummings
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA.,Henry Eyring Center for Cell & Genome Science, University of Utah, Salt Lake City, UT, USA
| | - Jessica M Deutsch
- School of Chemistry and Biochemistry, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Eoin Fahy
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Neha Garg
- School of Chemistry and Biochemistry, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Rachel Gregor
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jo Handelsman
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Mirtha Navarro-Hoyos
- BIoactivity for Sustainable Development Group (BIODESS), Department of Chemistry, University of Costa Rica, San Jose, Costa Rica
| | - Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Immunity, Inflammation, and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Scott A Jarmusch
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Katherine Louie
- DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Michael M Meijler
- Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva, Israel.,National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Itzhak Mizrahi
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel.,Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Rachel L Neve
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Trent R Northen
- DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Carlos Molina-Santiago
- Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Morgan Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Benjamin Pullman
- Center for Computational Mass Spectrometry, Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Aaron W Puri
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA.,Henry Eyring Center for Cell & Genome Science, University of Utah, Salt Lake City, UT, USA
| | - Robin Schmid
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Shankar Subramaniam
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Monica Thukral
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
| | - Felipe Vasquez-Castro
- Centro Nacional de Innovaciones Biotecnologicas (CENIBiot), CeNAT-CONARE, 1174-1200, San Jose, Costa Rica
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.,Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA. .,Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA.
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11
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Omenn GS, Lane L, Overall CM, Paik YK, Cristea IM, Corrales FJ, Lindskog C, Weintraub S, Roehrl MHA, Liu S, Bandeira N, Srivastava S, Chen YJ, Aebersold R, Moritz RL, Deutsch EW. Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project. J Proteome Res 2021; 20:5227-5240. [PMID: 34670092 DOI: 10.1021/acs.jproteome.1c00590] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The 2021 Metrics of the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 357 (92.8%) of the 19 778 predicted proteins coded in the human genome, a gain of 483 since 2020 from reports throughout the world reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 478 to 1421. This represents remarkable progress on the proteome parts list. The utilization of proteomics in a broad array of biological and clinical studies likewise continues to expand with many important findings and effective integration with other omics platforms. We present highlights from the Immunopeptidomics, Glycoproteomics, Infectious Disease, Cardiovascular, Musculo-Skeletal, Liver, and Cancers B/D-HPP teams and from the Knowledgebase, Mass Spectrometry, Antibody Profiling, and Pathology resource pillars, as well as ethical considerations important to the clinical utilization of proteomics and protein biomarkers.
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Affiliation(s)
- Gilbert S Omenn
- University of Michigan, Ann Arbor, Michigan 48109, United States.,Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | | | - Young-Ki Paik
- Yonsei Proteome Research Center and Yonsei University, Seoul 03722, Korea
| | - Ileana M Cristea
- Princeton University, Princeton, New Jersey 08544, United States
| | | | | | - Susan Weintraub
- University of Texas Health, San Antonio, San Antonio, Texas 78229-3900, United States
| | - Michael H A Roehrl
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Siqi Liu
- BGI Group, Shenzhen 518083, China
| | - Nuno Bandeira
- University of California, San Diego, La Jolla, California 92093, United States
| | | | - Yu-Ju Chen
- National Taiwan University, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Ruedi Aebersold
- ETH-Zurich and University of Zurich, 8092 Zurich, Switzerland
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
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12
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Leao TF, Clark CM, Bauermeister A, Elijah EO, Gentry EC, Husband M, Oliveira MF, Bandeira N, Wang M, Dorrestein PC. Quick-start infrastructure for untargeted metabolomics analysis in GNPS. Nat Metab 2021; 3:880-882. [PMID: 34244695 PMCID: PMC8705952 DOI: 10.1038/s42255-021-00429-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Tiago F Leao
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Chase M Clark
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Anelize Bauermeister
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Emmanuel O Elijah
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Emily C Gentry
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Makhai Husband
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Michelli F Oliveira
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Nuno Bandeira
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Center for Computational Mass Spectrometry, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Center for Computational Mass Spectrometry, University of California San Diego, La Jolla, CA, USA.
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Departments of Pharmacology and Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
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13
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Deutsch EW, Perez-Riverol Y, Carver J, Kawano S, Mendoza L, Van Den Bossche T, Gabriels R, Binz PA, Pullman B, Sun Z, Shofstahl J, Bittremieux W, Mak TD, Klein J, Zhu Y, Lam H, Vizcaíno JA, Bandeira N. Universal Spectrum Identifier for mass spectra. Nat Methods 2021; 18:768-770. [PMID: 34183830 PMCID: PMC8405201 DOI: 10.1038/s41592-021-01184-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 05/10/2021] [Indexed: 02/03/2023]
Abstract
Mass spectra provide the ultimate evidence to support the findings of mass spectrometry proteomics studies in publications, and it is therefore crucial to be able to trace the conclusions back to the spectra. The Universal Spectrum Identifier (USI) provides a standardized mechanism for encoding a virtual path to any mass spectrum contained in datasets deposited to public proteomics repositories. USI enables greater transparency of spectral evidence, with more than 1 billion USI identifications from over 3 billion spectra already available through ProteomeXchange repositories.
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Affiliation(s)
- Eric W. Deutsch
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA,Address correspondence to: , Phone: 206-732-1200, Fax: 206-732-1299. , Phone: 858-534-8666
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Jeremy Carver
- Center for Computational Mass Spectrometry, Department of Computer Science and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 92093-0404, USA
| | - Shin Kawano
- Toyama University of International Studies, 930-1292 Toyama, Japan
| | - Luis Mendoza
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Tim Van Den Bossche
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Ralf Gabriels
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Pierre-Alain Binz
- Clinical Chemistry Service, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Benjamin Pullman
- Center for Computational Mass Spectrometry, Department of Computer Science and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 92093-0404, USA
| | - Zhi Sun
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Jim Shofstahl
- Thermo Fisher Scientific, 355 River Oaks Parkway San Jose, CA 95134, USA
| | - Wout Bittremieux
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA,Department of Computer Science, University of Antwerp, 2020 Antwerp, Belgium
| | - Tytus D. Mak
- Mass Spectrometry Data Center, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Joshua Klein
- Program for Bioinformatics, Boston University, Boston, MA 02215, USA
| | - Yunping Zhu
- National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, #38, Life Science Park, Changping District, Beijing 102206, China
| | - Henry Lam
- Department of Chemical and Biological Engineering, the Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, Department of Computer Science and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 92093-0404, USA,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA,Address correspondence to: , Phone: 206-732-1200, Fax: 206-732-1299. , Phone: 858-534-8666
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14
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Bandeira N, Deutsch EW, Kohlbacher O, Martens L, Vizcaíno JA. Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future. Mol Cell Proteomics 2021; 20:100071. [PMID: 33711481 PMCID: PMC8056256 DOI: 10.1016/j.mcpro.2021.100071] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 12/12/2022] Open
Abstract
Today it is the norm that all relevant proteomics data that support the conclusions in scientific publications are made available in public proteomics data repositories. However, given the increase in the number of clinical proteomics studies, an important emerging topic is the management and dissemination of clinical, and thus potentially sensitive, human proteomics data. Both in the United States and in the European Union, there are legal frameworks protecting the privacy of individuals. Implementing privacy standards for publicly released research data in genomics and transcriptomics has led to processes to control who may access the data, so-called "controlled access" data. In parallel with the technological developments in the field, it is clear that the privacy risks of sharing proteomics data need to be properly assessed and managed. In our view, the proteomics community must be proactive in addressing these issues. Yet a careful balance must be kept. On the one hand, neglecting to address the potential of identifiability in human proteomics data could lead to reputational damage of the field, while on the other hand, erecting barriers to open access to clinical proteomics data will inevitably reduce reuse of proteomics data and could substantially delay critical discoveries in biomedical research. In order to balance these apparently conflicting requirements for data privacy and efficient use and reuse of research efforts through the sharing of clinical proteomics data, development efforts will be needed at different levels including bioinformatics infrastructure, policymaking, and mechanisms of oversight.
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Affiliation(s)
- Nuno Bandeira
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, California, USA; Department Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, California, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, California, USA
| | | | - Oliver Kohlbacher
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany; Quantitative Biology Center, University of Tübingen, Tübingen, Germany; Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany; Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
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15
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Bittremieux W, Adams C, Laukens K, Dorrestein PC, Bandeira N. Open Science Resources for the Mass Spectrometry-Based Analysis of SARS-CoV-2. J Proteome Res 2021; 20:1464-1475. [PMID: 33605735 DOI: 10.1021/acs.jproteome.0c00929] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The SARS-CoV-2 virus is the causative agent of the 2020 pandemic leading to the COVID-19 respiratory disease. With many scientific and humanitarian efforts ongoing to develop diagnostic tests, vaccines, and treatments for COVID-19, and to prevent the spread of SARS-CoV-2, mass spectrometry research, including proteomics, is playing a role in determining the biology of this viral infection. Proteomics studies are starting to lead to an understanding of the roles of viral and host proteins during SARS-CoV-2 infection, their protein-protein interactions, and post-translational modifications. This is beginning to provide insights into potential therapeutic targets or diagnostic strategies that can be used to reduce the long-term burden of the pandemic. However, the extraordinary situation caused by the global pandemic is also highlighting the need to improve mass spectrometry data and workflow sharing. We therefore describe freely available data and computational resources that can facilitate and assist the mass spectrometry-based analysis of SARS-CoV-2. We exemplify this by reanalyzing a virus-host interactome data set to detect protein-protein interactions and identify host proteins that could potentially be used as targets for drug repurposing.
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Affiliation(s)
- Wout Bittremieux
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla 92093, California, United States.,Department of Computer Science, University of Antwerp, Antwerp 2020, Belgium
| | - Charlotte Adams
- Department of Computer Science, University of Antwerp, Antwerp 2020, Belgium
| | - Kris Laukens
- Department of Computer Science, University of Antwerp, Antwerp 2020, Belgium
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla 92093, California, United States
| | - Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla 92093, California, United States.,Department of Computer Science and Engineering, University of California San Diego, La Jolla 92093, California, United States
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16
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Hoopmann MR, Kusebauch U, Palmblad M, Bandeira N, Shteynberg DD, He L, Xia B, Stoychev SH, Omenn GS, Weintraub ST, Moritz RL. Insights from the First Phosphopeptide Challenge of the MS Resource Pillar of the HUPO Human Proteome Project. J Proteome Res 2020; 19:4754-4765. [PMID: 33166149 DOI: 10.1021/acs.jproteome.0c00648] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mass spectrometry has greatly improved the analysis of phosphorylation events in complex biological systems and on a large scale. Despite considerable progress, the correct identification of phosphorylated sites, their quantification, and their interpretation regarding physiological relevance remain challenging. The MS Resource Pillar of the Human Proteome Organization (HUPO) Human Proteome Project (HPP) initiated the Phosphopeptide Challenge as a resource to help the community evaluate methods, learn procedures and data analysis routines, and establish their own workflows by comparing results obtained from a standard set of 94 phosphopeptides (serine, threonine, tyrosine) and their nonphosphorylated counterparts mixed at different ratios in a neat sample and a yeast background. Participants analyzed both samples with their method(s) of choice to report the identification and site localization of these peptides, determine their relative abundances, and enrich for the phosphorylated peptides in the yeast background. We discuss the results from 22 laboratories that used a range of different methods, instruments, and analysis software. We reanalyzed submitted data with a single software pipeline and highlight the successes and challenges in correct phosphosite localization. All of the data from this collaborative endeavor are shared as a resource to encourage the development of even better methods and tools for diverse phosphoproteomic applications. All submitted data and search results were uploaded to MassIVE (https://massive.ucsd.edu/) as data set MSV000085932 with ProteomeXchange identifier PXD020801.
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Affiliation(s)
| | - Ulrike Kusebauch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Magnus Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093, United States
| | | | - Lingjie He
- Synpeptide Co., Ltd., Shanghai 201204, China
| | - Bin Xia
- Synpeptide Co., Ltd., Shanghai 201204, China
| | | | - Gilbert S Omenn
- Institute for Systems Biology, Seattle, Washington 98109, United States.,Departments of Computational Medicine and Bioinformatics, Internal Medicine, and Human Genetics and School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
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17
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Omenn GS, Lane L, Overall CM, Cristea IM, Corrales FJ, Lindskog C, Paik YK, Van Eyk JE, Liu S, Pennington SR, Snyder MP, Baker MS, Bandeira N, Aebersold R, Moritz RL, Deutsch EW. Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project. J Proteome Res 2020; 19:4735-4746. [PMID: 32931287 DOI: 10.1021/acs.jproteome.0c00485] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
According to the 2020 Metrics of the HUPO Human Proteome Project (HPP), expression has now been detected at the protein level for >90% of the 19 773 predicted proteins coded in the human genome. The HPP annually reports on progress made throughout the world toward credibly identifying and characterizing the complete human protein parts list and promoting proteomics as an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2020-01 classified 17 874 proteins as PE1, having strong protein-level evidence, up 180 from 17 694 one year earlier. These represent 90.4% of the 19 773 predicted coding genes (all PE1,2,3,4 proteins in neXtProt). Conversely, the number of neXtProt PE2,3,4 proteins, termed the "missing proteins" (MPs), was reduced by 230 from 2129 to 1899 since the neXtProt 2019-01 release. PeptideAtlas is the primary source of uniform reanalysis of raw mass spectrometry data for neXtProt, supplemented this year with extensive data from MassIVE. PeptideAtlas 2020-01 added 362 canonical proteins between 2019 and 2020 and MassIVE contributed 84 more, many of which converted PE1 entries based on non-MS evidence to the MS-based subgroup. The 19 Biology and Disease-driven B/D-HPP teams continue to pursue the identification of driver proteins that underlie disease states, the characterization of regulatory mechanisms controlling the functions of these proteins, their proteoforms, and their interactions, and the progression of transitions from correlation to coexpression to causal networks after system perturbations. And the Human Protein Atlas published Blood, Brain, and Metabolic Atlases.
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Affiliation(s)
- Gilbert S Omenn
- University of Michigan, Ann Arbor, Michigan 48109, United States.,Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | | | - Ileana M Cristea
- Princeton University, Princeton, New Jersey 08544, United States
| | | | | | | | | | - Siqi Liu
- BGI Group, Shenzhen 518083, China
| | | | | | - Mark S Baker
- Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Nuno Bandeira
- University of California, San Diego, La Jolla, California 92093, United States
| | - Ruedi Aebersold
- ETH-Zurich and University of Zurich, 8092 Zurich, Switzerland
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
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18
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Adhikari S, Nice EC, Deutsch EW, Lane L, Omenn GS, Pennington SR, Paik YK, Overall CM, Corrales FJ, Cristea IM, Van Eyk JE, Uhlén M, Lindskog C, Chan DW, Bairoch A, Waddington JC, Justice JL, LaBaer J, Rodriguez H, He F, Kostrzewa M, Ping P, Gundry RL, Stewart P, Srivastava S, Srivastava S, Nogueira FCS, Domont GB, Vandenbrouck Y, Lam MPY, Wennersten S, Vizcaino JA, Wilkins M, Schwenk JM, Lundberg E, Bandeira N, Marko-Varga G, Weintraub ST, Pineau C, Kusebauch U, Moritz RL, Ahn SB, Palmblad M, Snyder MP, Aebersold R, Baker MS. A high-stringency blueprint of the human proteome. Nat Commun 2020; 11:5301. [PMID: 33067450 PMCID: PMC7568584 DOI: 10.1038/s41467-020-19045-9] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 09/25/2020] [Indexed: 02/07/2023] Open
Abstract
The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. On the occasion of the HPP's tenth anniversary, we here report a 90.4% complete high-stringency human proteome blueprint. This knowledge is essential for discerning molecular processes in health and disease, as we demonstrate by highlighting potential roles the human proteome plays in our understanding, diagnosis and treatment of cancers, cardiovascular and infectious diseases.
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Affiliation(s)
- Subash Adhikari
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Edouard C Nice
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
- Faculty of Medicine, Nursing and Health Sciences, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Eric W Deutsch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Lydie Lane
- Faculty of Medicine, SIB-Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Michel-Servet 1, 1211, Geneva, Switzerland
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2218, USA
| | - Stephen R Pennington
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland
| | - Young-Ki Paik
- Yonsei Proteome Research Center, 50 Yonsei-ro, Sudaemoon-ku, Seoul, 120-749, South Korea
| | | | - Fernando J Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología-CSIC, Proteored-ISCIII, 28049, Madrid, Spain
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Jennifer E Van Eyk
- Cedars Sinai Medical Center, Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Los Angeles, CA, 90048, USA
| | - Mathias Uhlén
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Cecilia Lindskog
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, 75185, Uppsala, Sweden
| | - Daniel W Chan
- Department of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21224, USA
| | - Amos Bairoch
- Faculty of Medicine, SIB-Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Michel-Servet 1, 1211, Geneva, Switzerland
| | - James C Waddington
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland
| | - Joshua L Justice
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Joshua LaBaer
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Markus Kostrzewa
- Bruker Daltonik GmbH, Microbiology and Diagnostics, Fahrenheitstrasse, 428359, Bremen, Germany
| | - Peipei Ping
- Cardiac Proteomics and Signaling Laboratory, Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Rebekah L Gundry
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Peter Stewart
- Department of Chemical Pathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | | | - Sudhir Srivastava
- Cancer Biomarkers Research Branch, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Suite 5E136, Rockville, MD, 20852, USA
| | - Fabio C S Nogueira
- Proteomics Unit and Laboratory of Proteomics, Institute of Chemistry, Federal University of Rio de Janeiro, Av Athos da Silveria Ramos, 149, 21941-909, Rio de Janeiro, RJ, Brazil
| | - Gilberto B Domont
- Proteomics Unit and Laboratory of Proteomics, Institute of Chemistry, Federal University of Rio de Janeiro, Av Athos da Silveria Ramos, 149, 21941-909, Rio de Janeiro, RJ, Brazil
| | - Yves Vandenbrouck
- University of Grenoble Alpes, Inserm, CEA, IRIG-BGE, U1038, 38000, Grenoble, France
| | - Maggie P Y Lam
- Departments of Medicine-Cardiology and Biochemistry and Molecular Genetics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
- Consortium for Fibrosis Research and Translation, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Sara Wennersten
- Division of Cardiology, Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Juan Antonio Vizcaino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Marc Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Jochen M Schwenk
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, Mail Code 0404, La Jolla, CA, 92093-0404, USA
| | | | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center San Antonio, UT Health, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA
| | - Charles Pineau
- University of Rennes, Inserm, EHESP, IREST, UMR_S 1085, F-35042, Rennes, France
| | - Ulrike Kusebauch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Seong Beom Ahn
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Magnus Palmblad
- Leiden University Medical Center, Leiden, 2333, The Netherlands
| | - Michael P Snyder
- Department of Genetics, Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Ruedi Aebersold
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
- Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Mark S Baker
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia.
- Department of Genetics, Stanford School of Medicine, Stanford, CA, 94305, USA.
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19
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Choi M, Carver J, Chiva C, Tzouros M, Huang T, Tsai TH, Pullman B, Bernhardt OM, Hüttenhain R, Teo GC, Perez-Riverol Y, Muntel J, Müller M, Goetze S, Pavlou M, Verschueren E, Wollscheid B, Nesvizhskii AI, Reiter L, Dunkley T, Sabidó E, Bandeira N, Vitek O. MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets. Nat Methods 2020; 17:981-984. [PMID: 32929271 PMCID: PMC7541731 DOI: 10.1038/s41592-020-0955-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 08/13/2020] [Indexed: 11/09/2022]
Abstract
MassIVE.quant is a repository infrastructure and data resource for reproducible quantitative mass spectrometry-based proteomics, which is compatible with all mass spectrometry data acquisition types and computational analysis tools. A branch structure enables MassIVE.quant to systematically store raw experimental data, metadata of the experimental design, scripts of the quantitative analysis workflow, intermediate input and output files, as well as alternative reanalyses of the same dataset.
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Affiliation(s)
- Meena Choi
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Jeremy Carver
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Cristina Chiva
- Proteomics Unit, Center for Genomics Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | - Manuel Tzouros
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Ting Huang
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Tsung-Heng Tsai
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Benjamin Pullman
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | | | - Ruth Hüttenhain
- Department of Molecular and Cellular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Guo Ci Teo
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yasset Perez-Riverol
- Proteomics Services, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | - Maik Müller
- Department of Health Sciences and Technology, Institute of Translational Medicine, ETH, Zurich, Switzerland
| | - Sandra Goetze
- Department of Health Sciences and Technology, Institute of Translational Medicine, ETH, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Maria Pavlou
- Department of Health Sciences and Technology, Institute of Translational Medicine, ETH, Zurich, Switzerland
| | - Erik Verschueren
- Department of Molecular and Cellular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Bernd Wollscheid
- Department of Health Sciences and Technology, Institute of Translational Medicine, ETH, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | | | - Tom Dunkley
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Eduard Sabidó
- Proteomics Unit, Center for Genomics Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
| | - Olga Vitek
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA.
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20
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Jarmusch AK, Wang M, Aceves CM, Advani RS, Aguirre S, Aksenov AA, Aleti G, Aron AT, Bauermeister A, Bolleddu S, Bouslimani A, Caraballo Rodriguez AM, Chaar R, Coras R, Elijah EO, Ernst M, Gauglitz JM, Gentry EC, Husband M, Jarmusch SA, Jones KL, Kamenik Z, Le Gouellec A, Lu A, McCall LI, McPhail KL, Meehan MJ, Melnik AV, Menezes RC, Montoya Giraldo YA, Nguyen NH, Nothias LF, Nothias-Esposito M, Panitchpakdi M, Petras D, Quinn RA, Sikora N, van der Hooft JJJ, Vargas F, Vrbanac A, Weldon KC, Knight R, Bandeira N, Dorrestein PC. ReDU: a framework to find and reanalyze public mass spectrometry data. Nat Methods 2020; 17:901-904. [PMID: 32807955 DOI: 10.1038/s41592-020-0916-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 07/10/2020] [Indexed: 11/09/2022]
Abstract
We present ReDU ( https://redu.ucsd.edu/ ), a system for metadata capture of public mass spectrometry-based metabolomics data, with validated controlled vocabularies. Systematic capture of knowledge enables the reanalysis of public data and/or co-analysis of one's own data. ReDU enables multiple types of analyses, including finding chemicals and associated metadata, comparing the shared and different chemicals between groups of samples, and metadata-filtered, repository-scale molecular networking.
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Affiliation(s)
- Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Rohit S Advani
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Shaden Aguirre
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Alexander A Aksenov
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Gajender Aleti
- Department of Psychiatry, Stein Clinical Research, University of California, San Diego, La Jolla, CA, USA
| | - Allegra T Aron
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Anelize Bauermeister
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Sanjana Bolleddu
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Andres Mauricio Caraballo Rodriguez
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Rama Chaar
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Roxana Coras
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Emmanuel O Elijah
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Madeleine Ernst
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.,Center for Newborn Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Julia M Gauglitz
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Emily C Gentry
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Makhai Husband
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Scott A Jarmusch
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen, UK
| | - Kenneth L Jones
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Zdenek Kamenik
- Institute of Microbiology, Czech Academy of Sciences, Videnska, Czech Republic
| | - Audrey Le Gouellec
- TIMC-IMAG, Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, Grenoble, France
| | - Aileen Lu
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Laura-Isobel McCall
- Department of Chemistry and Biochemistry, Department of Microbiology and Plant Biology, and Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, USA
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Michael J Meehan
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Riya C Menezes
- Research Group Mass Spectrometry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Yessica Alejandra Montoya Giraldo
- Grupo de Investigación en Ciencias Biológicas y Bioprocesos (CIBIOP), Department of Biological Sciences, Universidad EAFIT, Medellín, Colombia
| | - Ngoc Hung Nguyen
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Louis Felix Nothias
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Mélissa Nothias-Esposito
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Morgan Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Robert A Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University, Lansing, MI, USA
| | - Nicole Sikora
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Justin J J van der Hooft
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
| | - Fernando Vargas
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.,Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Alison Vrbanac
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kelly C Weldon
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.,Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA. .,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA. .,Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA. .,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
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21
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Aron AT, Gentry EC, McPhail KL, Nothias LF, Nothias-Esposito M, Bouslimani A, Petras D, Gauglitz JM, Sikora N, Vargas F, van der Hooft JJJ, Ernst M, Kang KB, Aceves CM, Caraballo-Rodríguez AM, Koester I, Weldon KC, Bertrand S, Roullier C, Sun K, Tehan RM, Boya P CA, Christian MH, Gutiérrez M, Ulloa AM, Tejeda Mora JA, Mojica-Flores R, Lakey-Beitia J, Vásquez-Chaves V, Zhang Y, Calderón AI, Tayler N, Keyzers RA, Tugizimana F, Ndlovu N, Aksenov AA, Jarmusch AK, Schmid R, Truman AW, Bandeira N, Wang M, Dorrestein PC. Reproducible molecular networking of untargeted mass spectrometry data using GNPS. Nat Protoc 2020; 15:1954-1991. [PMID: 32405051 DOI: 10.1038/s41596-020-0317-5] [Citation(s) in RCA: 263] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 03/03/2020] [Indexed: 02/06/2023]
Abstract
Global Natural Product Social Molecular Networking (GNPS) is an interactive online small molecule-focused tandem mass spectrometry (MS2) data curation and analysis infrastructure. It is intended to provide as much chemical insight as possible into an untargeted MS2 dataset and to connect this chemical insight to the user's underlying biological questions. This can be performed within one liquid chromatography (LC)-MS2 experiment or at the repository scale. GNPS-MassIVE is a public data repository for untargeted MS2 data with sample information (metadata) and annotated MS2 spectra. These publicly accessible data can be annotated and updated with the GNPS infrastructure keeping a continuous record of all changes. This knowledge is disseminated across all public data; it is a living dataset. Molecular networking-one of the main analysis tools used within the GNPS platform-creates a structured data table that reflects the molecular diversity captured in tandem mass spectrometry experiments by computing the relationships of the MS2 spectra as spectral similarity. This protocol provides step-by-step instructions for creating reproducible, high-quality molecular networks. For training purposes, the reader is led through a 90- to 120-min procedure that starts by recalling an example public dataset and its sample information and proceeds to creating and interpreting a molecular network. Each data analysis job can be shared or cloned to disseminate the knowledge gained, thus propagating information that can lead to the discovery of molecules, metabolic pathways, and ecosystem/community interactions.
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Affiliation(s)
- Allegra T Aron
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Emily C Gentry
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Louis-Félix Nothias
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Mélissa Nothias-Esposito
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Amina Bouslimani
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Daniel Petras
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Julia M Gauglitz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Nicole Sikora
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Fernando Vargas
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Madeleine Ernst
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kyo Bin Kang
- College of Pharmacy, Sookmyung Women's University, Seoul, Korea
| | - Christine M Aceves
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Irina Koester
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kelly C Weldon
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center of Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Samuel Bertrand
- Groupe Mer, Molécules, Santé-EA 2160, UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes, Nantes, France
- ThalassOMICS Metabolomics Facility, Plateforme Corsaire, Biogenouest, Nantes, France
| | - Catherine Roullier
- College of Pharmacy, Sookmyung Women's University, Seoul, Korea
- ThalassOMICS Metabolomics Facility, Plateforme Corsaire, Biogenouest, Nantes, France
| | - Kunyang Sun
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Richard M Tehan
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Cristopher A Boya P
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, Nagarjuna Nagar, India
| | - Martin H Christian
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
| | - Marcelino Gutiérrez
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
| | | | | | - Randy Mojica-Flores
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
- Departamento de Química, Universidad Autónoma de Chiriquí (UNACHI), David, Chiriquí, Panama
| | - Johant Lakey-Beitia
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
| | - Victor Vásquez-Chaves
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
| | - Yilue Zhang
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
| | - Angela I Calderón
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
| | - Nicole Tayler
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, Nagarjuna Nagar, India
| | - Robert A Keyzers
- School of Chemical & Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Fidele Tugizimana
- Centre for Plant Metabolomics Research, Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
- International R&D Division, Omnia Group (Pty) Ltd., Johannesburg, South Africa
| | - Nombuso Ndlovu
- Centre for Plant Metabolomics Research, Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
| | - Alexander A Aksenov
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Alan K Jarmusch
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Robin Schmid
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
| | - Mingxun Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, CA, USA.
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
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22
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Deutsch EW, Bandeira N, Sharma V, Perez-Riverol Y, Carver JJ, Kundu DJ, García-Seisdedos D, Jarnuczak AF, Hewapathirana S, Pullman BS, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, Hermjakob H, MacLean B, MacCoss MJ, Zhu Y, Ishihama Y, Vizcaíno JA. The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. Nucleic Acids Res 2020; 48:D1145-D1152. [PMID: 31686107 PMCID: PMC7145525 DOI: 10.1093/nar/gkz984] [Citation(s) in RCA: 316] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/11/2019] [Accepted: 10/14/2019] [Indexed: 11/24/2022] Open
Abstract
The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) has standardized data submission and dissemination of mass spectrometry proteomics data worldwide since 2012. In this paper, we describe the main developments since the previous update manuscript was published in Nucleic Acids Research in 2017. Since then, in addition to the four PX existing members at the time (PRIDE, PeptideAtlas including the PASSEL resource, MassIVE and jPOST), two new resources have joined PX: iProX (China) and Panorama Public (USA). We first describe the updated submission guidelines, now expanded to include six members. Next, with current data submission statistics, we demonstrate that the proteomics field is now actively embracing public open data policies. At the end of June 2019, more than 14 100 datasets had been submitted to PX resources since 2012, and from those, more than 9 500 in just the last three years. In parallel, an unprecedented increase of data re-use activities in the field, including 'big data' approaches, is enabling novel research and new data resources. At last, we also outline some of our future plans for the coming years.
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Affiliation(s)
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Department Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | | | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jeremy J Carver
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Department Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Deepti J Kundu
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - David García-Seisdedos
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Andrew F Jarnuczak
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Suresh Hewapathirana
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Benjamin S Pullman
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Department Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Julie Wertz
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Department Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Zhi Sun
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Shin Kawano
- Faculty of Contemporary Society, Toyama University of International Studies, Toyama 930–1292, Japan
- Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Chiba 277–0871, Japan
| | - Shujiro Okuda
- Niigata University Graduate School of Medical and Dental Sciences, Niigata 951–8510, Japan
| | - Yu Watanabe
- Niigata University Graduate School of Medical and Dental Sciences, Niigata 951–8510, Japan
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing 102206, China
| | | | | | - Yunping Zhu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing 102206, China
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606–8501, Japan
| | - Juan A Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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23
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Wang M, Jarmusch AK, Vargas F, Aksenov AA, Gauglitz JM, Weldon K, Petras D, da Silva R, Quinn R, Melnik AV, van der Hooft JJJ, Caraballo-Rodríguez AM, Nothias LF, Aceves CM, Panitchpakdi M, Brown E, Di Ottavio F, Sikora N, Elijah EO, Labarta-Bajo L, Gentry EC, Shalapour S, Kyle KE, Puckett SP, Watrous JD, Carpenter CS, Bouslimani A, Ernst M, Swafford AD, Zúñiga EI, Balunas MJ, Klassen JL, Loomba R, Knight R, Bandeira N, Dorrestein PC. Mass spectrometry searches using MASST. Nat Biotechnol 2020; 38:23-26. [PMID: 31894142 PMCID: PMC7236533 DOI: 10.1038/s41587-019-0375-9] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Ometa Labs LLC, San Diego, CA, USA
| | - Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Fernando Vargas
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Alexander A Aksenov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Julia M Gauglitz
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kelly Weldon
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ricardo da Silva
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Robert Quinn
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Justin J J van der Hooft
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Andrés Mauricio Caraballo-Rodríguez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Louis Felix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Morgan Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth Brown
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Francesca Di Ottavio
- Faculty of Bioscience and Technology for Food, Agriculture, and Environment, University of Teramo, Teramo, TE, Italy
| | - Nicole Sikora
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Emmanuel O Elijah
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Lara Labarta-Bajo
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Emily C Gentry
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Shabnam Shalapour
- Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kathleen E Kyle
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Sara P Puckett
- Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA
| | - Jeramie D Watrous
- Department of Medicine, University of California San Diego, San Diego, California, USA
| | - Carolina S Carpenter
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Madeleine Ernst
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Elina I Zúñiga
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Marcy J Balunas
- Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA
| | - Jonathan L Klassen
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Rohit Loomba
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.,Division of Gastroenterology, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Nuno Bandeira
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA. .,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA. .,Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA. .,Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
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24
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Deutsch EW, Lane L, Overall CM, Bandeira N, Baker MS, Pineau C, Moritz RL, Corrales F, Orchard S, Van Eyk JE, Paik YK, Weintraub ST, Vandenbrouck Y, Omenn GS. Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0. J Proteome Res 2019; 18:4108-4116. [PMID: 31599596 DOI: 10.1021/acs.jproteome.9b00542] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Human Proteome Organization's (HUPO) Human Proteome Project (HPP) developed Mass Spectrometry (MS) Data Interpretation Guidelines that have been applied since 2016. These guidelines have helped ensure that the emerging draft of the complete human proteome is highly accurate and with low numbers of false-positive protein identifications. Here, we describe an update to these guidelines based on consensus-reaching discussions with the wider HPP community over the past year. The revised 3.0 guidelines address several major and minor identified gaps. We have added guidelines for emerging data independent acquisition (DIA) MS workflows and for use of the new Universal Spectrum Identifier (USI) system being developed by the HUPO Proteomics Standards Initiative (PSI). In addition, we discuss updates to the standard HPP pipeline for collecting MS evidence for all proteins in the HPP, including refinements to minimum evidence. We present a new plan for incorporating MassIVE-KB into the HPP pipeline for the next (HPP 2020) cycle in order to obtain more comprehensive coverage of public MS data sets. The main checklist has been reorganized under headings and subitems, and related guidelines have been grouped. In sum, Version 2.1 of the HPP MS Data Interpretation Guidelines has served well, and this timely update to version 3.0 will aid the HPP as it approaches its goal of collecting and curating MS evidence of translation and expression for all predicted ∼20 000 human proteins encoded by the human genome.
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Affiliation(s)
- Eric W Deutsch
- Institute for Systems Biology , Seattle , Washington 98109 , United States
| | - Lydie Lane
- SIB Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, Faculty of Medicine , University of Geneva , CMU, Michel Servet 1 , 1211 Geneva 4 , Switzerland
| | - Christopher M Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, and Biochemistry & Molecular Biology, Faculty of Dentistry , The University of British Columbia , Vancouver , BC V6T 1Z4 , Canada
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry and Department of Computer Science and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California San Diego , La Jolla , California 92093 , United States
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Science , Macquarie University , Macquarie Park , NSW 2109 , Australia
| | - Charles Pineau
- Univ. Rennes , Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085 , F-35042 Rennes cedex , France
| | - Robert L Moritz
- Institute for Systems Biology , Seattle , Washington 98109 , United States
| | - Fernando Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología , Spanish Research Council , ProteoRed-.ISCIII , Madrid 117 , Spain
| | - Sandra Orchard
- European Molecular Biology Laboratory , European Bioinformatics Institute (EMBL-EBI) , Wellcome Trust Genome Campus , Hinxton , Cambridge CB10 1SD , U.K
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Department of Medicine , Cedars Sinai Medical Center , Los Angeles , California 90048 , United States
| | - Young-Ki Paik
- Yonsei Proteome Research Center , Yonsei University , 50 Yonsei-ro , Sudaemoon-ku , Seoul 03720 , Korea
| | - Susan T Weintraub
- The University of Texas Health Science Center at San Antonio , San Antonio , Texas 78229 , United States
| | - Yves Vandenbrouck
- Univ. Grenoble Alpes , CEA, INSERM, IRIG-BGE, U1038 , F-38000 Grenoble , France
| | - Gilbert S Omenn
- Institute for Systems Biology , Seattle , Washington 98109 , United States.,Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics and School of Public Health , University of Michigan , Ann Arbor , Michigan 48109-2218 , United States
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25
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Melnik AV, Vázquez-Baeza Y, Aksenov AA, Hyde E, McAvoy AC, Wang M, da Silva RR, Protsyuk I, Wu JV, Bouslimani A, Lim YW, Luzzatto-Knaan T, Comstock W, Quinn RA, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC, Garg N. Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis. mSystems 2019; 4:e00375-19. [PMID: 31551401 PMCID: PMC6759567 DOI: 10.1128/msystems.00375-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/02/2019] [Indexed: 02/07/2023] Open
Abstract
To visualize the personalized distributions of pathogens and chemical environments, including microbial metabolites, pharmaceuticals, and their metabolic products, within and between human lungs afflicted with cystic fibrosis (CF), we generated three-dimensional (3D) microbiome and metabolome maps of six explanted lungs from three cystic fibrosis patients. These 3D spatial maps revealed that the chemical environments differ between patients and within the lungs of each patient. Although the microbial ecosystems of the patients were defined by the dominant pathogen, their chemical diversity was not. Additionally, the chemical diversity between locales in the lungs of the same individual sometimes exceeded interindividual variation. Thus, the chemistry and microbiome of the explanted lungs appear to be not only personalized but also regiospecific. Previously undescribed analogs of microbial quinolones and antibiotic metabolites were also detected. Furthermore, mapping the chemical and microbial distributions allowed visualization of microbial community interactions, such as increased production of quorum sensing quinolones in locations where Pseudomonas was in contact with Staphylococcus and Granulicatella, consistent with in vitro observations of bacteria isolated from these patients. Visualization of microbe-metabolite associations within a host organ in early-stage CF disease in animal models will help elucidate the complex interplay between the presence of a given microbial structure, antibiotics, metabolism of antibiotics, microbial virulence factors, and host responses.IMPORTANCE Microbial infections are now recognized to be polymicrobial and personalized in nature. Comprehensive analysis and understanding of the factors underlying the polymicrobial and personalized nature of infections remain limited, especially in the context of the host. By visualizing microbiomes and metabolomes of diseased human lungs, we reveal how different the chemical environments are between hosts that are dominated by the same pathogen and how community interactions shape the chemical environment or vice versa. We highlight that three-dimensional organ mapping methods represent hypothesis-building tools that allow us to design mechanistic studies aimed at addressing microbial responses to other microbes, the host, and pharmaceutical drugs.
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Affiliation(s)
- Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Yoshiki Vázquez-Baeza
- Jacobs School of Engineering, University of California, San Diego, La Jolla, California, USA
- UC San Diego Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
| | - Alexander A Aksenov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Embriette Hyde
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Andrew C McAvoy
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Mingxun Wang
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, California, USA
| | - Ricardo R da Silva
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Ivan Protsyuk
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jason V Wu
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Yan Wei Lim
- Biology Department, San Diego State University, San Diego, California, USA
| | - Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - William Comstock
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Robert A Quinn
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Richard Wong
- Department of Pathology, University of California, San Diego, La Jolla, California, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Timothy Spivey
- Department of Radiology, University of California, San Diego, La Jolla, California, USA
| | - Sharon S Brouha
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Nuno Bandeira
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, California, USA
| | - Grace Y Lin
- Department of Pathology, University of California, San Diego, La Jolla, California, USA
| | - Forest Rohwer
- Biology Department, San Diego State University, San Diego, California, USA
| | - Douglas J Conrad
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Theodore Alexandrov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, California, USA
- UC San Diego Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Neha Garg
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
- Emory-Children's Center for Cystic Fibrosis and Airways Disease Research, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
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26
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Gauglitz JM, Aceves CM, Aksenov AA, Aleti G, Almaliti J, Bouslimani A, Brown EA, Campeau A, Caraballo-Rodríguez AM, Chaar R, da Silva RR, Demko AM, Di Ottavio F, Elijah E, Ernst M, Ferguson LP, Holmes X, Jarmusch AK, Jiang L, Kang KB, Koester I, Kwan B, Li J, Li Y, Melnik AV, Molina-Santiago C, Ni B, Oom AL, Panitchpakdi MW, Petras D, Quinn R, Sikora N, Spengler K, Teke B, Tripathi A, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vrbanac A, Vu AQ, Wang SC, Weldon K, Wilson K, Wozniak JM, Yoon M, Bandeira N, Dorrestein PC. Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages. Food Chem 2019; 302:125290. [PMID: 31404873 DOI: 10.1016/j.foodchem.2019.125290] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 07/19/2019] [Accepted: 07/28/2019] [Indexed: 10/26/2022]
Abstract
In our daily lives, we consume foods that have been transported, stored, prepared, cooked, or otherwise processed by ourselves or others. Food storage and preparation have drastic effects on the chemical composition of foods. Untargeted mass spectrometry analysis of food samples has the potential to increase our chemical understanding of these processes by detecting a broad spectrum of chemicals. We performed a time-based analysis of the chemical changes in foods during common preparations, such as fermentation, brewing, and ripening, using untargeted mass spectrometry and molecular networking. The data analysis workflow presented implements an approach to study changes in food chemistry that can reveal global alterations in chemical profiles, identify changes in abundance, as well as identify specific chemicals and their transformation products. The data generated in this study are publicly available, enabling the replication and re-analysis of these data in isolation, and serve as a baseline dataset for future investigations.
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Affiliation(s)
- Julia M Gauglitz
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Center for Microbiome Innovation, University of California, San Diego, United States.
| | - Christine M Aceves
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Alexander A Aksenov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Gajender Aleti
- Mammalian Genomics, J. Craig Venter Institute, San Diego, United States
| | - Jehad Almaliti
- Scripps Institution of Oceanography, University of California, San Diego, United States; Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan, Amman 11942, Jordan
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Elizabeth A Brown
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Anaamika Campeau
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Department of Pharmacology, University of California, San Diego, United States
| | - Andrés Mauricio Caraballo-Rodríguez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Rama Chaar
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Ricardo R da Silva
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Alyssa M Demko
- Scripps Institution of Oceanography, University of California, San Diego, United States
| | - Francesca Di Ottavio
- Faculty of Bioscience and Technology for Food, Agriculture, and Environment, University of Teramo, TE, Italy
| | - Emmanuel Elijah
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Madeleine Ernst
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - L Paige Ferguson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Xavier Holmes
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Lingjing Jiang
- Department of Family Medicine and Public Health, University of California, San Diego, United States
| | - Kyo Bin Kang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Irina Koester
- Scripps Institution of Oceanography, University of California, San Diego, United States
| | - Brian Kwan
- Department of Family Medicine and Public Health, University of California, San Diego, United States
| | - Jie Li
- Scripps Institution of Oceanography, University of California, San Diego, United States
| | - Yueying Li
- Scripps Institution of Oceanography, University of California, San Diego, United States
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Center for Microbiome Innovation, University of California, San Diego, United States
| | - Carlos Molina-Santiago
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071 Málaga, Spain
| | - Bohan Ni
- Scripps Institution of Oceanography, University of California, San Diego, United States
| | - Aaron L Oom
- Department of Medicine, University of California, San Diego, United States
| | - Morgan W Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Center for Microbiome Innovation, University of California, San Diego, United States; Scripps Institution of Oceanography, University of California, San Diego, United States
| | - Robert Quinn
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Nicole Sikora
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Katharina Spengler
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Bahar Teke
- Scripps Institution of Oceanography, University of California, San Diego, United States
| | - Anupriya Tripathi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Sabah Ul-Hasan
- School of Natural Sciences, University of California Merced, Merced, CA 95343, United States
| | - Justin J J van der Hooft
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Fernando Vargas
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Division of Biological Sciences, University of California at San Diego, La Jolla, CA, United States
| | - Alison Vrbanac
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, United States
| | - Anthony Q Vu
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, United States
| | - Steven C Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Division of Biological Sciences, University of California at San Diego, La Jolla, CA, United States
| | - Kelly Weldon
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Center for Microbiome Innovation, University of California, San Diego, United States
| | - Kayla Wilson
- Scripps Institution of Oceanography, University of California, San Diego, United States
| | - Jacob M Wozniak
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Department of Pharmacology, University of California, San Diego, United States
| | - Michael Yoon
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Department of Computer Science and Engineering, University of California, San Diego, United States
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Departments of Pharmacology and Pediatrics, University of California, San Diego, United States.
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27
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Quinn RA, Adem S, Mills RH, Comstock W, DeRight Goldasich L, Humphrey G, Aksenov AA, Melnik AV, da Silva R, Ackermann G, Bandeira N, Gonzalez DJ, Conrad D, O’Donoghue AJ, Knight R, Dorrestein PC. Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome. Microbiome 2019; 7:23. [PMID: 30760325 PMCID: PMC6375204 DOI: 10.1186/s40168-019-0636-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 01/29/2019] [Indexed: 05/31/2023]
Abstract
BACKGROUND Studies of the cystic fibrosis (CF) lung microbiome have consistently shown that lung function decline is associated with decreased microbial diversity due to the dominance of opportunistic pathogens. However, how this phenomenon is reflected in the metabolites and chemical environment of lung secretions remains poorly understood. METHODS Here we investigated the microbial and molecular composition of CF sputum samples using 16S rRNA gene amplicon sequencing and untargeted tandem mass spectrometry to determine their interrelationships and associations with clinical measures of disease severity. RESULTS The CF metabolome was found to exist in two states: one from patients with more severe disease that had higher molecular diversity and more Pseudomonas aeruginosa and the other from patients with better lung function having lower metabolite diversity and fewer pathogenic bacteria. The two molecular states were differentiated by the abundance and diversity of peptides and amino acids. Patients with severe disease and more pathogenic bacteria had higher levels of peptides. Analysis of the carboxyl terminal residues of these peptides indicated that neutrophil elastase and cathepsin G were responsible for their generation, and accordingly, these patients had higher levels of proteolytic activity from these enzymes in their sputum. The CF pathogen Pseudomonas aeruginosa was correlated with the abundance of amino acids and is known to primarily feed on them in the lung. CONCLUSIONS In cases of severe CF lung disease, proteolysis by host enzymes creates an amino acid-rich environment that P. aeruginosa comes to dominate, which may contribute to the pathogen's persistence by providing its preferred carbon source.
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Affiliation(s)
- Robert A. Quinn
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, 48823 MI USA
| | - Sandeep Adem
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
| | - Robert H. Mills
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA USA
| | - William Comstock
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
| | | | - Gregory Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, CA USA
| | - Alexander A. Aksenov
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
| | - Alexei V. Melnik
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
| | - Ricardo da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La Jolla, CA USA
| | - Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA USA
| | - David J. Gonzalez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA USA
| | - Doug Conrad
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA USA
- Department of Medicine, University of California San Diego, La Jolla, CA USA
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA USA
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA USA
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28
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Lambert JP, Picaud S, Fujisawa T, Hou H, Savitsky P, Uusküla-Reimand L, Gupta GD, Abdouni H, Lin ZY, Tucholska M, Knight JDR, Gonzalez-Badillo B, St-Denis N, Newman JA, Stucki M, Pelletier L, Bandeira N, Wilson MD, Filippakopoulos P, Gingras AC. Interactome Rewiring Following Pharmacological Targeting of BET Bromodomains. Mol Cell 2018; 73:621-638.e17. [PMID: 30554943 PMCID: PMC6375729 DOI: 10.1016/j.molcel.2018.11.006] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 09/06/2018] [Accepted: 11/02/2018] [Indexed: 12/20/2022]
Abstract
Targeting bromodomains (BRDs) of the bromo-and-extra-terminal (BET) family offers opportunities for therapeutic intervention in cancer and other diseases. Here, we profile the interactomes of BRD2, BRD3, BRD4, and BRDT following treatment with the pan-BET BRD inhibitor JQ1, revealing broad rewiring of the interaction landscape, with three distinct classes of behavior for the 603 unique interactors identified. A group of proteins associate in a JQ1-sensitive manner with BET BRDs through canonical and new binding modes, while two classes of extra-terminal (ET)-domain binding motifs mediate acetylation-independent interactions. Last, we identify an unexpected increase in several interactions following JQ1 treatment that define negative functions for BRD3 in the regulation of rRNA synthesis and potentially RNAPII-dependent gene expression that result in decreased cell proliferation. Together, our data highlight the contributions of BET protein modules to their interactomes allowing for a better understanding of pharmacological rewiring in response to JQ1.
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Affiliation(s)
- Jean-Philippe Lambert
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Sarah Picaud
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Takao Fujisawa
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Huayun Hou
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON, Canada
| | - Pavel Savitsky
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Liis Uusküla-Reimand
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON, Canada; Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Gagan D Gupta
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Hala Abdouni
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Monika Tucholska
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - James D R Knight
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | | | - Nicole St-Denis
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Joseph A Newman
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Manuel Stucki
- Department of Gynecology, University of Zurich, Wagistrasse 14, 8952 Schlieren, Switzerland
| | - Laurence Pelletier
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michael D Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON, Canada; Heart & Stroke Richard Lewar Centre of Excellence in Cardiovascular Research, Toronto, ON, Canada
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK; Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK.
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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29
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Deutsch EW, Perez-Riverol Y, Chalkley RJ, Wilhelm M, Tate S, Sachsenberg T, Walzer M, Käll L, Delanghe B, Böcker S, Schymanski EL, Wilmes P, Dorfer V, Kuster B, Volders PJ, Jehmlich N, Vissers JP, Wolan DW, Wang AY, Mendoza L, Shofstahl J, Dowsey AW, Griss J, Salek RM, Neumann S, Binz PA, Lam H, Vizcaíno JA, Bandeira N, Röst H. Expanding the Use of Spectral Libraries in Proteomics. J Proteome Res 2018; 17:4051-4060. [PMID: 30270626 PMCID: PMC6443480 DOI: 10.1021/acs.jproteome.8b00485] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The 2017 Dagstuhl Seminar on Computational Proteomics provided an opportunity for a broad discussion on the current state and future directions of the generation and use of peptide tandem mass spectrometry spectral libraries. Their use in proteomics is growing slowly, but there are multiple challenges in the field that must be addressed to further increase the adoption of spectral libraries and related techniques. The primary bottlenecks are the paucity of high quality and comprehensive libraries and the general difficulty of adopting spectral library searching into existing workflows. There are several existing spectral library formats, but none captures a satisfactory level of metadata; therefore, a logical next improvement is to design a more advanced, Proteomics Standards Initiative-approved spectral library format that can encode all of the desired metadata. The group discussed a series of metadata requirements organized into three designations of completeness or quality, tentatively dubbed bronze, silver, and gold. The metadata can be organized at four different levels of granularity: at the collection (library) level, at the individual entry (peptide ion) level, at the peak (fragment ion) level, and at the peak annotation level. Strategies for encoding mass modifications in a consistent manner and the requirement for encoding high-quality and commonly seen but as-yet-unidentified spectra were discussed. The group also discussed related topics, including strategies for comparing two spectra, techniques for generating representative spectra for a library, approaches for selection of optimal signature ions for targeted workflows, and issues surrounding the merging of two or more libraries into one. We present here a review of this field and the challenges that the community must address in order to accelerate the adoption of spectral libraries in routine analysis of proteomics datasets.
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Affiliation(s)
- Eric W. Deutsch
- Institute for Systems Biology, Seattle, Washington, 98109, United States
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Robert J. Chalkley
- University of California San Francisco, San Francisco, 94158, California, United States
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, 85354, Germany
| | | | - Timo Sachsenberg
- Department of Computer Science, Center for Bioinformatics, University of Tübingen, Sand 14, Tübingen, 72076, Germany
| | - Mathias Walzer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Lukas Käll
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH − Royal Institute of Technology, Stockholm 114 28, Sweden
| | - Bernard Delanghe
- Thermo Fisher Scientific Bremen, Hanna-Kunath Str. 11, 28199 Bremen, Germany
| | - Sebastian Böcker
- Chair for Bioinformatics, Friedrich-Schiller-University Jena, 07743 Jena, Germany
| | - Emma L. Schymanski
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Viktoria Dorfer
- University of Applied Sciences Upper Austria, Bioinformatics Research Group, Hagenberg, 4232, Austria
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, 85354, Germany
- Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich, Freising, 85354, Germany
| | | | - Nico Jehmlich
- Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | | | - Dennis W. Wolan
- Department of Molecular Medicine, The Scripps Research Institute, 92037, La Jolla, California, United States
| | - Ana Y. Wang
- Department of Molecular Medicine, The Scripps Research Institute, 92037, La Jolla, California, United States
| | - Luis Mendoza
- Institute for Systems Biology, Seattle, Washington, 98109, United States
| | - Jim Shofstahl
- Thermo Fisher Scientific, 355 River Oaks Parkway San Jose, CA 95134
| | - Andrew W. Dowsey
- Department of Population Health Sciences and Bristol Veterinary School, Faculty of Health Sciences, University of Bristol, Bristol BS9 1BN, UK
| | - Johannes Griss
- Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Währinger Gürtel 18-20, Vienna 1090, Austria
| | - Reza M. Salek
- The International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372 Lyon CEDEX 08, France
| | - Steffen Neumann
- Leibniz Institute of Plant Biochemistry, Department of Stress and Developmental Biology, 06120 Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Pierre-Alain Binz
- Clinical Chemistry Service, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
| | - Henry Lam
- Department of Chemical and Biological Engineering, the Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, Department of Computer Science and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 92093-0404, USA
| | - Hannes Röst
- The Donnelly Centre, University of Toronto, 160 College St., Toronto, ON, M5S 3E1, Canada
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30
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Pullman BS, Wertz J, Carver J, Bandeira N. ProteinExplorer: A Repository-Scale Resource for Exploration of Protein Detection in Public Mass Spectrometry Data Sets. J Proteome Res 2018; 17:4227-4234. [PMID: 30985146 DOI: 10.1021/acs.jproteome.8b00496] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
High-throughput tandem mass spectrometry has enabled the detection and identification of over 75% of all proteins predicted to result in translated gene products in the human genome. In fact, the galloping rate of data acquisition and sharing of mass spectrometry data has led to the current availability of many tens of terabytes of public data in thousands of human data sets. The systematic reanalysis of these public data sets has been used to build a community-scale spectral library of 2.1 million precursors for over 1 million unique sequences from over 19,000 proteins (including spectra of synthetic peptides). However, it has remained challenging to find and inspect spectra of peptides covering functional protein regions or matching novel proteins. ProteinExplorer addresses these challenges with an intuitive interface mapping tens of millions of identifications to functional sites on nearly all human proteins while maintaining provenance for every identification back to the original data set and data file. Additionally, ProteinExplorer facilitates the selection and inspection of HPP-compliant peptides whose spectra can be matched to spectra of synthetic peptides and already includes HPP-compliant evidence for 107 missing (PE2, PE3, and PE4) and 23 dubious (PE5) proteins. Finally, ProteinExplorer allows users to rate spectra and to contribute to a community library of peptides entitled PrEdict (Protein Existance dictionary) mapping to novel proteins but whose preliminary identities have not yet been fully established with community-scale false discovery rates and synthetic peptide spectra. ProteinExplorer can be now be accessed at https://massive.ucsd.edu/ProteoSAFe/protein_explorer_splash.jsp .
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31
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Scheubert K, Hufsky F, Petras D, Wang M, Nothias LF, Dührkop K, Bandeira N, Dorrestein PC, Böcker S. Significance estimation for large scale metabolomics annotations by spectral matching. Nat Commun 2017; 8:1494. [PMID: 29133785 PMCID: PMC5684233 DOI: 10.1038/s41467-017-01318-5] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/08/2017] [Indexed: 12/17/2022] Open
Abstract
The annotation of small molecules in untargeted mass spectrometry relies on the matching of fragment spectra to reference library spectra. While various spectrum-spectrum match scores exist, the field lacks statistical methods for estimating the false discovery rates (FDR) of these annotations. We present empirical Bayes and target-decoy based methods to estimate the false discovery rate (FDR) for 70 public metabolomics data sets. We show that the spectral matching settings need to be adjusted for each project. By adjusting the scoring parameters and thresholds, the number of annotations rose, on average, by +139% (ranging from −92 up to +5705%) when compared with a default parameter set available at GNPS. The FDR estimation methods presented will enable a user to assess the scoring criteria for large scale analysis of mass spectrometry based metabolomics data that has been essential in the advancement of proteomics, transcriptomics, and genomics science. Matching fragment spectra to reference library spectra is an important procedure for annotating small molecules in untargeted mass spectrometry based metabolomics studies. Here, the authors develop strategies to estimate false discovery rates (FDR) by empirical Bayes and target-decoy based methods which enable a user to define the scoring criteria for spectral matching.
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Affiliation(s)
- Kerstin Scheubert
- Chair for Bioinformatics, Friedrich Schiller University Jena, Jena, 07743, Germany
| | - Franziska Hufsky
- Chair for Bioinformatics, Friedrich Schiller University Jena, Jena, 07743, Germany.,RNA Bioinformatics and High Throughput Analysis, Friedrich Schiller University Jena, Jena, 07743, Germany
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA, 92093, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Louis-Félix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA, 92093, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Kai Dührkop
- Chair for Bioinformatics, Friedrich Schiller University Jena, Jena, 07743, Germany
| | - Nuno Bandeira
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA, 92093, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA, 92093, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Sebastian Böcker
- Chair for Bioinformatics, Friedrich Schiller University Jena, Jena, 07743, Germany.
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32
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Garg N, Wang M, Hyde E, da Silva RR, Melnik AV, Protsyuk I, Bouslimani A, Lim YW, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC. Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung. Cell Host Microbe 2017; 22:705-716.e4. [PMID: 29056429 DOI: 10.1016/j.chom.2017.10.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/12/2017] [Accepted: 09/14/2017] [Indexed: 12/12/2022]
Abstract
Our understanding of the spatial variation in the chemical and microbial makeup of an entire human organ remains limited, in part due to the size and heterogeneity of human organs and the complexity of the associated metabolome and microbiome. To address this challenge, we developed a workflow to enable the cartography of metabolomic and microbiome data onto a three-dimensional (3D) organ reconstruction built off radiological images. This enabled the direct visualization of the microbial and chemical makeup of a human lung from a cystic fibrosis patient. We detected host-derived molecules, microbial metabolites, medications, and region-specific metabolism of medications and placed it in the context of microbial distributions in the lung. Our tool further created browsable maps of a 3D microbiome/metabolome reconstruction map on a radiological image of a human lung and forms an interactive resource for the scientific community.
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Affiliation(s)
- Neha Garg
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mingxun Wang
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Embriette Hyde
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ricardo R da Silva
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ivan Protsyuk
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yan Wei Lim
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Richard Wong
- Department of Pathology, University of California, San Diego Health, San Diego, CA 92103, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Timothy Spivey
- Department of Radiology, University of California, San Diego Health, San Diego, CA 92103, USA
| | - Sharon S Brouha
- Department of Radiology, University of California, San Diego Health, San Diego, CA 92103, USA
| | - Nuno Bandeira
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Grace Y Lin
- Department of Pathology, University of California, San Diego Health, San Diego, CA 92103, USA
| | - Forest Rohwer
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Douglas J Conrad
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Theodore Alexandrov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany.
| | - Rob Knight
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA.
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33
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Trevisan-Silva D, Bednaski AV, Fischer JSG, Veiga SS, Bandeira N, Guthals A, Marchini FK, Leprevost FV, Barbosa VC, Senff-Ribeiro A, Carvalho PC. A multi-protease, multi-dissociation, bottom-up-to-top-down proteomic view of the Loxosceles intermedia venom. Sci Data 2017; 4:170090. [PMID: 28696408 PMCID: PMC5505115 DOI: 10.1038/sdata.2017.90] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 05/12/2017] [Indexed: 12/15/2022] Open
Abstract
Venoms are a rich source for the discovery of molecules with biotechnological applications, but their analysis is challenging even for state-of-the-art proteomics. Here we report on a large-scale proteomic assessment of the venom of Loxosceles intermedia, the so-called brown spider. Venom was extracted from 200 spiders and fractioned into two aliquots relative to a 10 kDa cutoff mass. Each of these was further fractioned and digested with trypsin (4 h), trypsin (18 h), pepsin (18 h), and chymotrypsin (18 h), then analyzed by MudPIT on an LTQ-Orbitrap XL ETD mass spectrometer fragmenting precursors by CID, HCD, and ETD. Aliquots of undigested samples were also analyzed. Our experimental design allowed us to apply spectral networks, thus enabling us to obtain meta-contig assemblies, and consequently de novo sequencing of practically complete proteins, culminating in a deep proteome assessment of the venom. Data are available via ProteomeXchange, with identifier PXD005523.
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Affiliation(s)
- Dilza Trevisan-Silva
- Department of Cell Biology, Federal University of Paraná, Curitiba 81531-980, Brazil
| | - Aline V Bednaski
- Department of Cell Biology, Federal University of Paraná, Curitiba 81531-980, Brazil
| | - Juliana S G Fischer
- Computational Mass Spectrometry &Proteomics Group, Carlos Chagas Institute, Fiocruz, Curitiba 81.350-010, Brazil
| | - Silvio S Veiga
- Department of Cell Biology, Federal University of Paraná, Curitiba 81531-980, Brazil
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, University of California, San Diego 92093-0404, USA
| | - Adrian Guthals
- Center for Computational Mass Spectrometry, University of California, San Diego 92093-0404, USA
| | - Fabricio K Marchini
- Functional Genomics Laboratory, Carlos Chagas Institute, Fiocruz, Curitiba 81.350-010, Brazil.,Mass Spectrometry Facility RPT02H, Carlos Chagas Institute, Fiocruz, Curitiba 81.350-010, Brazil
| | - Felipe V Leprevost
- Computational Mass Spectrometry &Proteomics Group, Carlos Chagas Institute, Fiocruz, Curitiba 81.350-010, Brazil
| | - Valmir C Barbosa
- Systems Engineering and Computer Science Program, COPPE, Federal University of Rio de Janeiro, Rio de Janeiro 21941-914, Brazil
| | - Andrea Senff-Ribeiro
- Department of Cell Biology, Federal University of Paraná, Curitiba 81531-980, Brazil
| | - Paulo C Carvalho
- Computational Mass Spectrometry &Proteomics Group, Carlos Chagas Institute, Fiocruz, Curitiba 81.350-010, Brazil.,Laboratory of Toxinology, Fiocruz, Rio de Janeiro 21040-900, Brazil
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34
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Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol 2017; 34:828-837. [PMID: 27504778 DOI: 10.1038/nbt.3597] [Citation(s) in RCA: 2254] [Impact Index Per Article: 322.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 05/10/2016] [Indexed: 12/14/2022]
Abstract
The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.
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Affiliation(s)
- Mingxun Wang
- Computer Science and Engineering, UC San Diego, La Jolla, United States.,Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Jeremy J Carver
- Computer Science and Engineering, UC San Diego, La Jolla, United States.,Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Vanessa V Phelan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Laura M Sanchez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Neha Garg
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Yao Peng
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Don Duy Nguyen
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Jeramie Watrous
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Clifford A Kapono
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Carla Porto
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Michael J Meehan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Wei-Ting Liu
- Department of Microbiology and Immunology, Stanford University, Palo Alto, United States
| | - Max Crüsemann
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Paul D Boudreau
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | | | | | | | - Laura A Pace
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Robert A Quinn
- Biology Department, San Diego State University, San Diego, United States
| | - Katherine R Duncan
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Cheng-Chih Hsu
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Dimitrios J Floros
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Ronnie G Gavilan
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Karin Kleigrewe
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Trent Northen
- Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Rachel J Dutton
- FAS Center for Systems Biology, Harvard, Cambridge, United States
| | - Delphine Parrot
- Produits naturels - Synthèses - Chimie Médicinale, University of Rennes 1, Rennes Cedex, France
| | - Erin E Carlson
- Chemistry, University of Minnesota, Minneapolis, United States
| | - Bertrand Aigle
- Dynamique des Génomes et Adaptation Microbienne, University of Lorraine, Vandœuvre-lès-Nancy, France
| | | | - Lars Jelsbak
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Christian Sohlenkamp
- Centro de Ciencias Genómicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Mexico
| | - Pavel Pevzner
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States.,Computer Science and Engineering, UC San Diego, La Jolla, United States
| | - Anna Edlund
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, United States.,School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Jeffrey McLean
- Department of Periodontics, University of Washington, Seattle, United States.,School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Jörn Piel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Brian T Murphy
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois Chicago, Chicago, United States
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Chih-Chuang Liaw
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | - Maria Maansson
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Robert A Keyzers
- School of Chemical & Physical Sciences, and Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Amy C Sims
- Gillings School of Global Public Health, Department of Epidemiology, UNC Chapel Hill, Chapel Hill, United States
| | - Andrew R Johnson
- Department of Chemistry, Indiana University, Bloomington, United States
| | | | - Brian E Sedio
- Smithsonian Tropical Research Institute, Ancón, Panama.,Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Andreas Klitgaard
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Charles B Larson
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Cristopher A Boya P
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | | | - David J Gonzalez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Denise B Silva
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil.,Centro de Ciencias Biologicas e da Saude, Universidade Fderal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Lucas M Marques
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Daniel P Demarque
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Egle Pociute
- Sirenas Marine Discovery, San Diego, United States
| | - Ellis C O'Neill
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Enora Briand
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,UMR CNRS 6553 ECOBIO, University of Rennes 1, Rennes Cedex, France
| | | | - Eve A Granatosky
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, United States
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Florian Ryffel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | - Hosein Mohimani
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Jenan J Kharbush
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Yi Zeng
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | | | - Kenji L Kurita
- PBSci-Chemistry & Biochemistry Department, UC Santa Cruz, Santa Cruz, United States
| | - Pep Charusanti
- Department of Bioengineering, UC San Diego, La Jolla, United States
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, United States
| | | | - Lisa Vuong
- Sirenas Marine Discovery, San Diego, United States
| | - Maryam Elfeki
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois Chicago, Chicago, United States
| | - Matthew F Traxler
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, United States
| | - Niclas Engene
- Department of Biological Sciences, Florida International University, Miami, United States
| | - Nobuhiro Koyama
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Oliver B Vining
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, United States
| | - Ralph Baric
- Gillings School of Global Public Health, Department of Epidemiology, UNC Chapel Hill, Chapel Hill, United States
| | - Ricardo R Silva
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Samantha J Mascuch
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Sophie Tomasi
- Produits naturels - Synthèses - Chimie Médicinale, University of Rennes 1, Rennes Cedex, France
| | - Stefan Jenkins
- Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, United States
| | | | - Thomas Hoffman
- Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
| | - Vinayak Agarwal
- Center for Oceans and Human Health, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Philip G Williams
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Jingqui Dai
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Ram Neupane
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Joshua Gurr
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Andrés M C Rodríguez
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Anne Lamsa
- Division of Biological Sciences, UC San Diego, La Jolla, United States
| | - Chen Zhang
- Department of Nanoengineering, UC San Diego, La Jolla, United States
| | - Kathleen Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Brendan M Duggan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Jehad Almaliti
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Prasad Phapale
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Louis-Felix Nothias
- Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Labex CEBA, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Theodore Alexandrov
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Labex CEBA, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Jennifer E Kyle
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Thomas O Metz
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Tyler Peryea
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Dac-Trung Nguyen
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Danielle VanLeer
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Paul Shinn
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Rolf Müller
- Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
| | - Katrina M Waters
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Wenyuan Shi
- School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Xueting Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lixin Zhang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Rob Knight
- Department of Pediatrics, UC San Diego, La Jolla, United States
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | | | - Kit Pogliano
- Division of Biological Sciences, UC San Diego, La Jolla, United States
| | - Roger G Linington
- PBSci-Chemistry & Biochemistry Department, UC Santa Cruz, Santa Cruz, United States
| | - Marcelino Gutiérrez
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Norberto P Lopes
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - William H Gerwick
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Bradley S Moore
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Center for Oceans and Human Health, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
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35
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Luzzatto-Knaan T, Garg N, Wang M, Glukhov E, Peng Y, Ackermann G, Amir A, Duggan BM, Ryazanov S, Gerwick L, Knight R, Alexandrov T, Bandeira N, Gerwick WH, Dorrestein PC. Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae. eLife 2017; 6. [PMID: 28492366 PMCID: PMC5441867 DOI: 10.7554/elife.24214] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 04/29/2017] [Indexed: 12/13/2022] Open
Abstract
Natural product screening programs have uncovered molecules from diverse natural sources with various biological activities and unique structures. However, much is yet underexplored and additional information is hidden in these exceptional collections. We applied untargeted mass spectrometry approaches to capture the chemical space and dispersal patterns of metabolites from an in-house library of marine cyanobacterial and algal collections. Remarkably, 86% of the metabolomics signals detected were not found in other available datasets of similar nature, supporting the hypothesis that marine cyanobacteria and algae possess distinctive metabolomes. The data were plotted onto a world map representing eight major sampling sites, and revealed potential geographic locations with high chemical diversity. We demonstrate the use of these inventories as a tool to explore the diversity and distribution of natural products. Finally, we utilized this tool to guide the isolation of a new cyclic lipopeptide, yuvalamide A, from a marine cyanobacterium. DOI:http://dx.doi.org/10.7554/eLife.24214.001 Cyanobacteria and algae are found in all oceans around the globe. Like plants, they can use sunlight as a source of energy in a process called photosynthesis. As a result, these organisms are important sources of oxygen and another vital nutrient called nitrogen for other marine organisms. Many of these organisms also produce a variety of other chemicals known as “natural products” to help them to survive in their environments. Some of these natural products have shown potential as medicinal drugs. The search for new chemicals with useful medicinal properties has led researchers to collect samples of algae and cyanobacteria from various locations around the world. An approach called mass spectrometry is often used to identify new chemicals because it can provide information about the structure of a molecule based on how much its fragments weigh. Luzzatto-Knaan et al. used mass spectrometry to search for new chemicals in samples of algae and cyanobacteria that had been collected by diving and snorkeling in a wide variety of tropical marine environments over several decades. The experiments reveal that the organisms in these samples produce a diverse range of chemicals, most of which were previously unknown and have not been found in other similar environmental collections. The data were grouped together into eight major collection areas covering different parts of the tropics. The samples from some areas contained a wider variety of chemicals than others. Within each collection area, some molecules were found to be very common whereas others were only present at specific locations. To highlight the distribution of these natural products, Luzzatto-Knaan et al. display the data on a world map. Further experiments used this approach as a guide to extract a previously unknown chemical called yuvalamide A from a marine cyanobacterium. The next challenge would be to associate the geographical patterns of chemicals to their potential ecological roles. This approach offers a new way to explore large-scale collections of environmental samples to discover and study new natural products. DOI:http://dx.doi.org/10.7554/eLife.24214.002
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Affiliation(s)
- Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States
| | - Neha Garg
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States
| | - Mingxun Wang
- Center for Computational Mass Spectrometry and Department of Computer Science and Engineering, University of California San Diego, San Diego, United States
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, San Diego, United States
| | - Yao Peng
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, United States
| | - Gail Ackermann
- Departments of Pediatrics and Computer Science and Engineering, University of California San Diego, San Diego, United States
| | - Amnon Amir
- Departments of Pediatrics and Computer Science and Engineering, University of California San Diego, San Diego, United States
| | - Brendan M Duggan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States
| | | | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, San Diego, United States
| | - Rob Knight
- Departments of Pediatrics and Computer Science and Engineering, University of California San Diego, San Diego, United States
| | - Theodore Alexandrov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States.,European Molecular Biology Laboratory, Heidelberg, Germany
| | - Nuno Bandeira
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States.,Center for Computational Mass Spectrometry and Department of Computer Science and Engineering, University of California San Diego, San Diego, United States
| | - William H Gerwick
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, San Diego, United States
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States.,Center for Computational Mass Spectrometry and Department of Computer Science and Engineering, University of California San Diego, San Diego, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, San Diego, United States
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36
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Petras D, Nothias LF, Quinn RA, Alexandrov T, Bandeira N, Bouslimani A, Castro-Falcón G, Chen L, Dang T, Floros DJ, Hook V, Garg N, Hoffner N, Jiang Y, Kapono CA, Koester I, Knight R, Leber CA, Ling TJ, Luzzatto-Knaan T, McCall LI, McGrath AP, Meehan MJ, Merritt JK, Mills RH, Morton J, Podvin S, Protsyuk I, Purdy T, Satterfield K, Searles S, Shah S, Shires S, Steffen D, White M, Todoric J, Tuttle R, Wojnicz A, Sapp V, Vargas F, Yang J, Zhang C, Dorrestein PC. Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats. Anal Chem 2016; 88:10775-10784. [PMID: 27732780 PMCID: PMC6326777 DOI: 10.1021/acs.analchem.6b03456] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The cars we drive, the homes we live in, the restaurants we visit, and the laboratories and offices we work in are all a part of the modern human habitat. Remarkably, little is known about the diversity of chemicals present in these environments and to what degree molecules from our bodies influence the built environment that surrounds us and vice versa. We therefore set out to visualize the chemical diversity of five built human habitats together with their occupants, to provide a snapshot of the various molecules to which humans are exposed on a daily basis. The molecular inventory was obtained through untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis of samples from each human habitat and from the people that occupy those habitats. Mapping MS-derived data onto 3D models of the environments showed that frequently touched surfaces, such as handles (e.g., door, bicycle), resemble the molecular fingerprint of the human skin more closely than other surfaces that are less frequently in direct contact with humans (e.g., wall, bicycle frame). Approximately 50% of the MS/MS spectra detected were shared between people and the environment. Personal care products, plasticizers, cleaning supplies, food, food additives, and even medications that were found to be a part of the human habitat. The annotations indicate that significant transfer of chemicals takes place between us and our built environment. The workflows applied here will lay the foundation for future studies of molecular distributions in medical, forensic, architectural, space exploration, and environmental applications.
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Affiliation(s)
- Daniel Petras
- UCSD Collaborative Mass Spectrometry Innovation Center, 9500 Gilman Drive, La Jolla, CA 92093, USA
- UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Louis-Félix Nothias
- UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Robert A. Quinn
- UCSD Collaborative Mass Spectrometry Innovation Center, 9500 Gilman Drive, La Jolla, CA 92093, USA
- UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Theodore Alexandrov
- UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Structural and Computational Biology, EMBL, Meyerhofstr. 1, 69117 Heidelberg, Germany
- SCiLS GmbH, Fahrenheitstr. 1, 28359 Bremen, Germany
| | - Nuno Bandeira
- UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, 9500 Gilman Drive, La Jolla, CA 92093, USA
- UCSD Department of Computer Science, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Amina Bouslimani
- UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | | | - Liangyu Chen
- UCSD Collaborative Mass Spectrometry Innovation Center, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Tam Dang
- UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, 9500 Gilman Drive, La Jolla, CA 92093, USA
- TU Berlin, Institut für Chemie, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Dimitrios J Floros
- UCSD Collaborative Mass Spectrometry Innovation Center, 9500 Gilman Drive, La Jolla, CA 92093, USA
- UCSD Chemistry and Biochemistry, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Vivian Hook
- UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Neha Garg
- UCSD Collaborative Mass Spectrometry Innovation Center, 9500 Gilman Drive, La Jolla, CA 92093, USA
- UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Nicole Hoffner
- UCSD Neurosciences Graduate Program, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yike Jiang
- UCSD Biological Sciences Graduate Program, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Clifford A. Kapono
- UCSD Chemistry and Biochemistry, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Irina Koester
- Scripps Institution of Oceanography, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Rob Knight
- UCSD Department of Computer Science, 9500 Gilman Drive, La Jolla, CA 92093, USA
- UCSD Department of Pediatrics, 9500 Gilman Drive, La Jolla, CA 92093, USA
- UCSD center for Microbiome Innovation, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Christopher A Leber
- Scripps Institution of Oceanography, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Tie-Jun Ling
- UCSD Collaborative Mass Spectrometry Innovation Center, 9500 Gilman Drive, La Jolla, CA 92093, USA
- UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, 9500 Gilman Drive, La Jolla, CA 92093, USA
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 West Changjiang Rd. Hefei 230036, P. R. China
| | - Tal Luzzatto-Knaan
- UCSD Collaborative Mass Spectrometry Innovation Center, 9500 Gilman Drive, La Jolla, CA 92093, USA
- UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Laura-Isobel McCall
- UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Aaron P. McGrath
- UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Michael J. Meehan
- UCSD Collaborative Mass Spectrometry Innovation Center, 9500 Gilman Drive, La Jolla, CA 92093, USA
- UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jonathan K. Merritt
- UCSD Neurosciences Graduate Program, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Robert H. Mills
- UCSD Biomedical Sciences Graduate Program, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jamie Morton
- UCSD Department of Computer Science, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Sonia Podvin
- UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Ivan Protsyuk
- Structural and Computational Biology, EMBL, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Trevor Purdy
- Scripps Institution of Oceanography, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Kendall Satterfield
- UCSD Biomedical Sciences Graduate Program, 9500 Gilman Drive, La Jolla, CA 92093, USA
- UCSD Department of Pharmacology, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Stephen Searles
- UCSD Department of Pathology, 9500 Gilman Drive, La Jolla, CA 92093, USA
- UCSD Biomedical Sciences Graduate Program, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Sahil Shah
- UCSD Neurosciences Graduate Program, 9500 Gilman Drive, La Jolla, CA 92093, USA
- UCSD School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Sarah Shires
- UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, 9500 Gilman Drive, La Jolla, CA 92093, USA
- UCSD Biomedical Sciences Graduate Program, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Dana Steffen
- UCSD Biomedical Sciences Graduate Program, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Margot White
- Scripps Institution of Oceanography, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jelena Todoric
- UCSD Department of Pharmacology, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Robert Tuttle
- Scripps Institution of Oceanography, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Aneta Wojnicz
- Facultad de Medicina de la Universidad Autónoma de Madrid. Calle del Arzobispo Morcillo 4. 28029 Madrid, Spain
| | - Valerie Sapp
- UCSD Biomedical Sciences Graduate Program, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Fernando Vargas
- UCSD Biological Sciences Graduate Program, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jin Yang
- UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Chao Zhang
- UCSD Bioengineering Undergraduate Program, 9500 Gilman Drive, La Jolla, CA 92093, USA
- UCSD Mathematics Undergraduate Program, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Pieter C. Dorrestein
- UCSD Collaborative Mass Spectrometry Innovation Center, 9500 Gilman Drive, La Jolla, CA 92093, USA
- UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, 9500 Gilman Drive, La Jolla, CA 92093, USA
- UCSD center for Microbiome Innovation, 9500 Gilman Drive, La Jolla, CA 92093, USA
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37
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Wohlgemuth G, Mehta SS, Mejia RF, Neumann S, Pedrosa D, Pluskal T, Schymanski EL, Willighagen EL, Wilson M, Wishart DS, Arita M, Dorrestein PC, Bandeira N, Wang M, Schulze T, Salek RM, Steinbeck C, Nainala VC, Mistrik R, Nishioka T, Fiehn O. SPLASH, a hashed identifier for mass spectra. Nat Biotechnol 2016; 34:1099-1101. [PMID: 27824832 PMCID: PMC5515539 DOI: 10.1038/nbt.3689] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Gert Wohlgemuth
- West Coast Metabolomics Center and Genome Center University of California Davis, Davis, CA, USA
| | - Sajjan S. Mehta
- West Coast Metabolomics Center and Genome Center University of California Davis, Davis, CA, USA
| | - Ramon F. Mejia
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Steffen Neumann
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Diego Pedrosa
- West Coast Metabolomics Center and Genome Center University of California Davis, Davis, CA, USA
| | - Tomáš Pluskal
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA, USA
| | - Emma L. Schymanski
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Egon L. Willighagen
- Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, The Netherlands
| | - Michael Wilson
- Department of Computing Science, University of Alberta, Edmonton, AB, Canada
| | - David S. Wishart
- Department of Computing Science, University of Alberta, Edmonton, AB, Canada
| | - Masanori Arita
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
- National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, CA, USA
- Departments of Pharmacology and Pediatrics, School of Medicine, UC San Diego, La Jolla, CA, USA
| | - Nuno Bandeira
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, CA, USA
- Computer Science and Engineering, UC San Diego, La Jolla, CA, USA
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Computer Science and Engineering, UC San Diego, La Jolla, CA, USA
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, CA, USA
| | - Tobias Schulze
- Department of Effect-Directed Analysis, UFZ Helmholtz Centre for Environmental Research GmbH, Leipzig, Germany
| | - Reza M. Salek
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Christoph Steinbeck
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Venkata Chandrasekhar Nainala
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | - Takaaki Nishioka
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Kyoto, Japan
| | - Oliver Fiehn
- West Coast Metabolomics Center and Genome Center University of California Davis, Davis, CA, USA
- Biochemistry Department, King Abdulaziz University, Jeddah, Saudi Arabia
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38
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Abstract
One direct route for the discovery of therapeutic human monoclonal antibodies (mAbs) involves the isolation of peripheral B cells from survivors/sero-positive individuals after exposure to an infectious reagent or disease etiology, followed by single-cell sequencing or hybridoma generation. Peripheral B cells, however, are not always easy to obtain and represent only a small percentage of the total B-cell population across all bodily tissues. Although it has been demonstrated that tandem mass spectrometry (MS/MS) techniques can interrogate the full polyclonal antibody (pAb) response to an antigen in vivo, all current approaches identify MS/MS spectra against databases derived from genetic sequencing of B cells from the same patient. In this proof-of-concept study, we demonstrate the feasibility of a novel MS/MS antibody discovery approach in which only serum antibodies are required without the need for sequencing of genetic material. Peripheral pAbs from a cytomegalovirus-exposed individual were purified by glycoprotein B antigen affinity and de novo sequenced from MS/MS data. Purely MS-derived mAbs were then manufactured in mammalian cells to validate potency via antigen-binding ELISA. Interestingly, we found that these mAbs accounted for 1 to 2% of total donor IgG but were not detected in parallel sequencing of memory B cells from the same patient.
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Affiliation(s)
- Adrian Guthals
- Mapp Biopharmaceutical, Inc. , 6160 Lusk Boulevard #C105, San Diego, California 92121, United States
| | - Yutian Gan
- Department of Proteomics & Biological Resources, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Laura Murray
- Department of Protein Chemistry, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Yongmei Chen
- Department of Antibody Engineering, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Jeremy Stinson
- Department of Molecular Biology, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Gerald Nakamura
- Department of Antibody Engineering, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Jennie R Lill
- Department of Proteomics & Biological Resources, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Wendy Sandoval
- Department of Proteomics & Biological Resources, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California, San Diego , 9500 Gilman Drive, Mail Code 0404, La Jolla, California 92093, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , 9500 Gilman Drive, Mail Code 0657, La Jolla, California 92093, United States
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39
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Deutsch EW, Csordas A, Sun Z, Jarnuczak A, Perez-Riverol Y, Ternent T, Campbell DS, Bernal-Llinares M, Okuda S, Kawano S, Moritz RL, Carver JJ, Wang M, Ishihama Y, Bandeira N, Hermjakob H, Vizcaíno JA. The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. Nucleic Acids Res 2016; 45:D1100-D1106. [PMID: 27924013 PMCID: PMC5210636 DOI: 10.1093/nar/gkw936] [Citation(s) in RCA: 648] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 10/07/2016] [Indexed: 11/13/2022] Open
Abstract
The ProteomeXchange (PX) Consortium of proteomics resources (http://www.proteomexchange.org) was formally started in 2011 to standardize data submission and dissemination of mass spectrometry proteomics data worldwide. We give an overview of the current consortium activities and describe the advances of the past few years. Augmenting the PX founding members (PRIDE and PeptideAtlas, including the PASSEL resource), two new members have joined the consortium: MassIVE and jPOST. ProteomeCentral remains as the common data access portal, providing the ability to search for data sets in all participating PX resources, now with enhanced data visualization components. We describe the updated submission guidelines, now expanded to include four members instead of two. As demonstrated by data submission statistics, PX is supporting a change in culture of the proteomics field: public data sharing is now an accepted standard, supported by requirements for journal submissions resulting in public data release becoming the norm. More than 4500 data sets have been submitted to the various PX resources since 2012. Human is the most represented species with approximately half of the data sets, followed by some of the main model organisms and a growing list of more than 900 diverse species. Data reprocessing activities are becoming more prominent, with both MassIVE and PeptideAtlas releasing the results of reprocessed data sets. Finally, we outline the upcoming advances for ProteomeXchange.
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Affiliation(s)
| | - Attila Csordas
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Zhi Sun
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Andrew Jarnuczak
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Tobias Ternent
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Manuel Bernal-Llinares
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Shujiro Okuda
- Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Shin Kawano
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Kashiwa 277-0871, Japan
| | | | - Jeremy J Carver
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.,Department Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Mingxun Wang
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.,Department Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.,Department Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,National Center for Protein Sciences, Beijing, China
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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40
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Na S, Payne SH, Bandeira N. Multi-species Identification of Polymorphic Peptide Variants via Propagation in Spectral Networks. Mol Cell Proteomics 2016; 15:3501-3512. [PMID: 27609420 PMCID: PMC5098046 DOI: 10.1074/mcp.o116.060913] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Indexed: 11/25/2022] Open
Abstract
Peptide and protein identification remains challenging in organisms with poorly annotated or rapidly evolving genomes, as are commonly encountered in environmental or biofuels research. Such limitations render tandem mass spectrometry (MS/MS) database search algorithms ineffective as they lack corresponding sequences required for peptide-spectrum matching. We address this challenge with the spectral networks approach to (1) match spectra of orthologous peptides across multiple related species and then (2) propagate peptide annotations from identified to unidentified spectra. We here present algorithms to assess the statistical significance of spectral alignments (Align-GF), reduce the impurity in spectral networks, and accurately estimate the error rate in propagated identifications. Analyzing three related Cyanothece species, a model organism for biohydrogen production, spectral networks identified peptides from highly divergent sequences from networks with dozens of variant peptides, including thousands of peptides in species lacking a sequenced genome. Our analysis further detected the presence of many novel putative peptides even in genomically characterized species, thus suggesting the possibility of gaps in our understanding of their proteomic and genomic expression. A web-based pipeline for spectral networks analysis is available at http://proteomics.ucsd.edu/software.
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Affiliation(s)
- Seungjin Na
- From the ‡Dept. of Computer Science and Engineering, University of California, San Diego, La Jolla, California, 92093.,§Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, California, 92093
| | - Samuel H Payne
- ¶Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Nuno Bandeira
- From the ‡Dept. of Computer Science and Engineering, University of California, San Diego, La Jolla, California, 92093; .,§Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, California, 92093.,‖Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, 92093
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41
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Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol 2016. [PMID: 27504778 DOI: 10.1038/nbt.3597.sharing] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.
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Affiliation(s)
- Mingxun Wang
- Computer Science and Engineering, UC San Diego, La Jolla, United States.,Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Jeremy J Carver
- Computer Science and Engineering, UC San Diego, La Jolla, United States.,Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Vanessa V Phelan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Laura M Sanchez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Neha Garg
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Yao Peng
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Don Duy Nguyen
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Jeramie Watrous
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Clifford A Kapono
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Carla Porto
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Michael J Meehan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Wei-Ting Liu
- Department of Microbiology and Immunology, Stanford University, Palo Alto, United States
| | - Max Crüsemann
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Paul D Boudreau
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | | | | | | | - Laura A Pace
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Robert A Quinn
- Biology Department, San Diego State University, San Diego, United States
| | - Katherine R Duncan
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Cheng-Chih Hsu
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Dimitrios J Floros
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Ronnie G Gavilan
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Karin Kleigrewe
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Trent Northen
- Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Rachel J Dutton
- FAS Center for Systems Biology, Harvard, Cambridge, United States
| | - Delphine Parrot
- Produits naturels - Synthèses - Chimie Médicinale, University of Rennes 1, Rennes Cedex, France
| | - Erin E Carlson
- Chemistry, University of Minnesota, Minneapolis, United States
| | - Bertrand Aigle
- Dynamique des Génomes et Adaptation Microbienne, University of Lorraine, Vandœuvre-lès-Nancy, France
| | | | - Lars Jelsbak
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Christian Sohlenkamp
- Centro de Ciencias Genómicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Mexico
| | - Pavel Pevzner
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States.,Computer Science and Engineering, UC San Diego, La Jolla, United States
| | - Anna Edlund
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, United States.,School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Jeffrey McLean
- Department of Periodontics, University of Washington, Seattle, United States.,School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Jörn Piel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Brian T Murphy
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois Chicago, Chicago, United States
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Chih-Chuang Liaw
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | - Maria Maansson
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Robert A Keyzers
- School of Chemical & Physical Sciences, and Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Amy C Sims
- Gillings School of Global Public Health, Department of Epidemiology, UNC Chapel Hill, Chapel Hill, United States
| | - Andrew R Johnson
- Department of Chemistry, Indiana University, Bloomington, United States
| | | | - Brian E Sedio
- Smithsonian Tropical Research Institute, Ancón, Panama.,Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Andreas Klitgaard
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Charles B Larson
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Cristopher A Boya P
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | | | - David J Gonzalez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Denise B Silva
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil.,Centro de Ciencias Biologicas e da Saude, Universidade Fderal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Lucas M Marques
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Daniel P Demarque
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Egle Pociute
- Sirenas Marine Discovery, San Diego, United States
| | - Ellis C O'Neill
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Enora Briand
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,UMR CNRS 6553 ECOBIO, University of Rennes 1, Rennes Cedex, France
| | | | - Eve A Granatosky
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, United States
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Florian Ryffel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | - Hosein Mohimani
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Jenan J Kharbush
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Yi Zeng
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | | | - Kenji L Kurita
- PBSci-Chemistry & Biochemistry Department, UC Santa Cruz, Santa Cruz, United States
| | - Pep Charusanti
- Department of Bioengineering, UC San Diego, La Jolla, United States
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, United States
| | | | - Lisa Vuong
- Sirenas Marine Discovery, San Diego, United States
| | - Maryam Elfeki
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois Chicago, Chicago, United States
| | - Matthew F Traxler
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, United States
| | - Niclas Engene
- Department of Biological Sciences, Florida International University, Miami, United States
| | - Nobuhiro Koyama
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Oliver B Vining
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, United States
| | - Ralph Baric
- Gillings School of Global Public Health, Department of Epidemiology, UNC Chapel Hill, Chapel Hill, United States
| | - Ricardo R Silva
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Samantha J Mascuch
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Sophie Tomasi
- Produits naturels - Synthèses - Chimie Médicinale, University of Rennes 1, Rennes Cedex, France
| | - Stefan Jenkins
- Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, United States
| | | | - Thomas Hoffman
- Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
| | - Vinayak Agarwal
- Center for Oceans and Human Health, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Philip G Williams
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Jingqui Dai
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Ram Neupane
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Joshua Gurr
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Andrés M C Rodríguez
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Anne Lamsa
- Division of Biological Sciences, UC San Diego, La Jolla, United States
| | - Chen Zhang
- Department of Nanoengineering, UC San Diego, La Jolla, United States
| | - Kathleen Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Brendan M Duggan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Jehad Almaliti
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Prasad Phapale
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Louis-Felix Nothias
- Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Labex CEBA, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Theodore Alexandrov
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Labex CEBA, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Jennifer E Kyle
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Thomas O Metz
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Tyler Peryea
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Dac-Trung Nguyen
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Danielle VanLeer
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Paul Shinn
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Rolf Müller
- Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
| | - Katrina M Waters
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Wenyuan Shi
- School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Xueting Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lixin Zhang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Rob Knight
- Department of Pediatrics, UC San Diego, La Jolla, United States
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | | | - Kit Pogliano
- Division of Biological Sciences, UC San Diego, La Jolla, United States
| | - Roger G Linington
- PBSci-Chemistry & Biochemistry Department, UC Santa Cruz, Santa Cruz, United States
| | - Marcelino Gutiérrez
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Norberto P Lopes
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - William H Gerwick
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Bradley S Moore
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Center for Oceans and Human Health, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
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Nasir W, Toledo AG, Noborn F, Nilsson J, Wang M, Bandeira N, Larson G. SweetNET: A Bioinformatics Workflow for Glycopeptide MS/MS Spectral Analysis. J Proteome Res 2016; 15:2826-40. [PMID: 27399812 DOI: 10.1021/acs.jproteome.6b00417] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Glycoproteomics has rapidly become an independent analytical platform bridging the fields of glycomics and proteomics to address site-specific protein glycosylation and its impact in biology. Current glycopeptide characterization relies on time-consuming manual interpretations and demands high levels of personal expertise. Efficient data interpretation constitutes one of the major challenges to be overcome before true high-throughput glycopeptide analysis can be achieved. The development of new glyco-related bioinformatics tools is thus of crucial importance to fulfill this goal. Here we present SweetNET: a data-oriented bioinformatics workflow for efficient analysis of hundreds of thousands of glycopeptide MS/MS-spectra. We have analyzed MS data sets from two separate glycopeptide enrichment protocols targeting sialylated glycopeptides and chondroitin sulfate linkage region glycopeptides, respectively. Molecular networking was performed to organize the glycopeptide MS/MS data based on spectral similarities. The combination of spectral clustering, oxonium ion intensity profiles, and precursor ion m/z shift distributions provided typical signatures for the initial assignment of different N-, O- and CS-glycopeptide classes and their respective glycoforms. These signatures were further used to guide database searches leading to the identification and validation of a large number of glycopeptide variants including novel deoxyhexose (fucose) modifications in the linkage region of chondroitin sulfate proteoglycans.
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Affiliation(s)
- Waqas Nasir
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg , SE 413 45 Gothenburg, Sweden
| | - Alejandro Gomez Toledo
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg , SE 413 45 Gothenburg, Sweden
| | - Fredrik Noborn
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg , SE 413 45 Gothenburg, Sweden
| | - Jonas Nilsson
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg , SE 413 45 Gothenburg, Sweden
| | - Mingxun Wang
- Department of Computer Science and Engineering, Center for Computational Mass Spectrometry, CSE, and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , La Jolla, California 92093, United States
| | - Nuno Bandeira
- Department of Computer Science and Engineering, Center for Computational Mass Spectrometry, CSE, and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , La Jolla, California 92093, United States
| | - Göran Larson
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg , SE 413 45 Gothenburg, Sweden
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43
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Kulkarni S, Koller A, Mani KM, Wen R, Alfieri A, Saha S, Wang J, Patel P, Bandeira N, Guha C, Chen EI. Identifying Urinary and Serum Exosome Biomarkers for Radiation Exposure Using a Data Dependent Acquisition and SWATH-MS Combined Workflow. Int J Radiat Oncol Biol Phys 2016; 96:566-77. [PMID: 27485285 DOI: 10.1016/j.ijrobp.2016.06.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 05/25/2016] [Accepted: 06/07/2016] [Indexed: 02/06/2023]
Abstract
PURPOSE Early and accurate assessment of radiation injury by radiation-responsive biomarkers is critical for triage and early intervention. Biofluids such as urine and serum are convenient for such analysis. Recent research has also suggested that exosomes are a reliable source of biomarkers in disease progression. In the present study, we analyzed total urine proteome and exosomes isolated from urine or serum for potential biomarkers of acute and persistent radiation injury in mice exposed to lethal whole body irradiation (WBI). METHODS AND MATERIALS For feasibility studies, the mice were irradiated at 10.4 Gy WBI, and urine and serum samples were collected 24 and 72 hours after irradiation. Exosomes were isolated and analyzed using liquid chromatography mass spectrometry/mass spectrometry-based workflow for radiation exposure signatures. A data dependent acquisition and SWATH-MS combined workflow approach was used to identify significantly exosome biomarkers indicative of acute or persistent radiation-induced responses. For the validation studies, mice were exposed to 3, 6, 8, or 10 Gy WBI, and samples were analyzed for comparison. RESULTS A comparison between total urine proteomics and urine exosome proteomics demonstrated that exosome proteomic analysis was superior in identifying radiation signatures. Feasibility studies identified 23 biomarkers from urine and 24 biomarkers from serum exosomes after WBI. Urinary exosome signatures identified different physiological parameters than the ones obtained in serum exosomes. Exosome signatures from urine indicated injury to the liver, gastrointestinal, and genitourinary tracts. In contrast, serum showed vascular injuries and acute inflammation in response to radiation. Selected urinary exosomal biomarkers also showed changes at lower radiation doses in validation studies. CONCLUSIONS Exosome proteomics revealed radiation- and time-dependent protein signatures after WBI. A total of 47 differentially secreted proteins were identified in urinary and serum exosomes. Together, these data showed the feasibility of defining biomarkers that could elucidate tissue-associated and systemic response caused by high-dose ionizing radiation. This is the first report using an exosome proteomics approach to identify radiation signatures.
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Affiliation(s)
- Shilpa Kulkarni
- Department of Radiation Oncology, Albert Einstein College of Medicine, Bronx, New York
| | - Antonius Koller
- Proteomics Center, Stony Brook University School of Medicine, Stony Brook, New York; Proteomics Shared Resource, Herbert Irving Comprehensive Cancer Center, New York, New York
| | - Kartik M Mani
- Department of Radiation Oncology, Albert Einstein College of Medicine, Bronx, New York
| | - Ruofeng Wen
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York
| | - Alan Alfieri
- Department of Radiation Oncology, Albert Einstein College of Medicine, Bronx, New York
| | - Subhrajit Saha
- Department of Radiation Oncology, Albert Einstein College of Medicine, Bronx, New York
| | - Jian Wang
- Center for Computational Mass Spectrometry, University of California, San Diego, California; Department of Computer Science and Engineering, University of California, San Diego, California
| | - Purvi Patel
- Proteomics Shared Resource, Herbert Irving Comprehensive Cancer Center, New York, New York; Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, University of California, San Diego, California; Department of Computer Science and Engineering, University of California, San Diego, California; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California
| | - Chandan Guha
- Department of Radiation Oncology, Albert Einstein College of Medicine, Bronx, New York.
| | - Emily I Chen
- Proteomics Center, Stony Brook University School of Medicine, Stony Brook, New York; Proteomics Shared Resource, Herbert Irving Comprehensive Cancer Center, New York, New York; Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York; Department of Pharmacology, Columbia University Medical Center, New York, New York.
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44
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Liu G, Knight JDR, Zhang JP, Tsou CC, Wang J, Lambert JP, Larsen B, Tyers M, Raught B, Bandeira N, Nesvizhskii AI, Choi H, Gingras AC. Data Independent Acquisition analysis in ProHits 4.0. J Proteomics 2016; 149:64-68. [PMID: 27132685 DOI: 10.1016/j.jprot.2016.04.042] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 03/18/2016] [Accepted: 04/27/2016] [Indexed: 11/30/2022]
Abstract
Affinity purification coupled with mass spectrometry (AP-MS) is a powerful technique for the identification and quantification of physical interactions. AP-MS requires careful experimental design, appropriate control selection and quantitative workflows to successfully identify bona fide interactors amongst a large background of contaminants. We previously introduced ProHits, a Laboratory Information Management System for interaction proteomics, which tracks all samples in a mass spectrometry facility, initiates database searches and provides visualization tools for spectral counting-based AP-MS approaches. More recently, we implemented Significance Analysis of INTeractome (SAINT) within ProHits to provide scoring of interactions based on spectral counts. Here, we provide an update to ProHits to support Data Independent Acquisition (DIA) with identification software (DIA-Umpire and MSPLIT-DIA), quantification tools (through DIA-Umpire, or externally via targeted extraction), and assessment of quantitative enrichment (through mapDIA) and scoring of interactions (through SAINT-intensity). With additional improvements, notably support of the iProphet pipeline, facilitated deposition into ProteomeXchange repositories and enhanced export and viewing functions, ProHits 4.0 offers a comprehensive suite of tools to facilitate affinity proteomics studies. SIGNIFICANCE It remains challenging to score, annotate and analyze proteomics data in a transparent manner. ProHits was previously introduced as a LIMS to enable storing, tracking and analysis of standard AP-MS data. In this revised version, we expand ProHits to include integration with a number of identification and quantification tools based on Data-Independent Acquisition (DIA). ProHits 4.0 also facilitates data deposition into public repositories, and the transfer of data to new visualization tools.
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Affiliation(s)
- Guomin Liu
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - James D R Knight
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Jian Ping Zhang
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Chih-Chiang Tsou
- Department of Pathology, University of Michigan, Ann Arbor, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA
| | - Jian Wang
- Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, California, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
| | - Jean-Philippe Lambert
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Brett Larsen
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
| | - Brian Raught
- Princess Margaret Cancer Institute, Department of Medical Biophysics, University of Toronto, Ontario, Canada
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, California, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA
| | - Hyungwon Choi
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research, Singapore, Singapore
| | - Anne-Claude Gingras
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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45
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Hook V, Bandeira N. Neuropeptidomics Mass Spectrometry Reveals Signaling Networks Generated by Distinct Protease Pathways in Human Systems. J Am Soc Mass Spectrom 2015; 26:1970-80. [PMID: 26483184 PMCID: PMC4749436 DOI: 10.1007/s13361-015-1251-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 07/30/2015] [Accepted: 08/05/2015] [Indexed: 05/23/2023]
Abstract
Neuropeptides regulate intercellular signaling as neurotransmitters of the central and peripheral nervous systems, and as peptide hormones in the endocrine system. Diverse neuropeptides of distinct primary sequences of various lengths, often with post-translational modifications, coordinate and integrate regulation of physiological functions. Mass spectrometry-based analysis of the diverse neuropeptide structures in neuropeptidomics research is necessary to define the full complement of neuropeptide signaling molecules. Human neuropeptidomics has notable importance in defining normal and dysfunctional neuropeptide signaling in human health and disease. Neuropeptidomics has great potential for expansion in translational research opportunities for defining neuropeptide mechanisms of human diseases, providing novel neuropeptide drug targets for drug discovery, and monitoring neuropeptides as biomarkers of drug responses. In consideration of the high impact of human neuropeptidomics for health, an observed gap in this discipline is the few published articles in human neuropeptidomics compared with, for example, human proteomics and related mass spectrometry disciplines. Focus on human neuropeptidomics will advance new knowledge of the complex neuropeptide signaling networks participating in the fine control of neuroendocrine systems. This commentary review article discusses several human neuropeptidomics accomplishments that illustrate the rapidly expanding diversity of neuropeptides generated by protease processing of pro-neuropeptide precursors occurring within the secretory vesicle proteome. Of particular interest is the finding that human-specific cathepsin V participates in producing enkephalin and likely other neuropeptides, indicating unique proteolytic mechanisms for generating human neuropeptides. The field of human neuropeptidomics has great promise to solve new mechanisms in disease conditions, leading to new drug targets and therapeutic agents for human diseases. Graphical Abstract ᅟ.
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Affiliation(s)
- Vivian Hook
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093-0719, USA.
- School of Medicine, Department of Neurosciences and Department of Pharmacology, University of California, San Diego, La Jolla, CA, 92093-0719, USA.
| | - Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093-0719, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, 92093-0719, USA
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46
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Abstract
Tandem mass (MS/MS) spectrometry has become the method of choice for protein identification and has launched a quest for the identification of every translated protein and peptide. However, computational developments have lagged behind the pace of modern data acquisition protocols and have become a major bottleneck in proteomics analysis of complex samples. As it stands today, attempts to identify MS/MS spectra against large databases (e.g., the human microbiome or 6-frame translation of the human genome) face a search space that is 10-100 times larger than the human proteome, where it becomes increasingly challenging to separate between true and false peptide matches. As a result, the sensitivity of current state-of-the-art database search methods drops by nearly 38% to such low identification rates that almost 90% of all MS/MS spectra are left as unidentified. We address this problem by extending the generating function approach to rigorously compute the joint spectral probability of multiple spectra being matched to peptides with overlapping sequences, thus enabling the confident assignment of higher significance to overlapping peptide-spectrum matches (PSMs). We find that these joint spectral probabilities can be several orders of magnitude more significant than individual PSMs, even in the ideal case when perfect separation between signal and noise peaks could be achieved per individual MS/MS spectrum. After benchmarking this approach on a typical lysate MS/MS dataset, we show that the proposed intersecting spectral probabilities for spectra from overlapping peptides improve peptide identification by 30-62%.
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Affiliation(s)
- Adrian Guthals
- Department of Computer Science and Engineering, University of California–San Diego, La Jolla, California
| | - Christina Boucher
- Department of Computer Science, Colorado State University, Fort Collins, Colorado
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California–San Diego, La Jolla, California
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California–San Diego, La Jolla, California
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47
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Duncan KR, Crüsemann M, Lechner A, Sarkar A, Li J, Ziemert N, Wang M, Bandeira N, Moore BS, Dorrestein PC, Jensen PR. Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species. ACTA ACUST UNITED AC 2015; 22:460-471. [PMID: 25865308 DOI: 10.1016/j.chembiol.2015.03.010] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/26/2015] [Accepted: 03/10/2015] [Indexed: 12/12/2022]
Abstract
Genome sequencing has revealed that bacteria contain many more biosynthetic gene clusters than predicted based on the number of secondary metabolites discovered to date. While this biosynthetic reservoir has fostered interest in new tools for natural product discovery, there remains a gap between gene cluster detection and compound discovery. Here we apply molecular networking and the new concept of pattern-based genome mining to 35 Salinispora strains, including 30 for which draft genome sequences were either available or obtained for this study. The results provide a method to simultaneously compare large numbers of complex microbial extracts, which facilitated the identification of media components, known compounds and their derivatives, and new compounds that could be prioritized for structure elucidation. These efforts revealed considerable metabolite diversity and led to several molecular family-gene cluster pairings, of which the quinomycin-type depsipeptide retimycin A was characterized and linked to gene cluster NRPS40 using pattern-based bioinformatic approaches.
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Affiliation(s)
- Katherine R Duncan
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Max Crüsemann
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Anna Lechner
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Anindita Sarkar
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Jie Li
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Nadine Ziemert
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Mingxun Wang
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Bradley S Moore
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, Departments of Pharmacology, Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Departments of Pharmacology, Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
| | - Paul R Jensen
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA.
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48
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Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolomé S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol 2015; 32:223-6. [PMID: 24727771 PMCID: PMC3986813 DOI: 10.1038/nbt.2839] [Citation(s) in RCA: 2143] [Impact Index Per Article: 238.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Juan A Vizcaíno
- 1] European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. [2]
| | - Eric W Deutsch
- 1] Institute for Systems Biology, Seattle, Washington, USA. [2]
| | - Rui Wang
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Attila Csordas
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Florian Reisinger
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Daniel Ríos
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - José A Dianes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Zhi Sun
- Institute for Systems Biology, Seattle, Washington, USA
| | - Terry Farrah
- Institute for Systems Biology, Seattle, Washington, USA
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, California, USA
| | - Pierre-Alain Binz
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Ioannis Xenarios
- 1] Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland. [2] University of Lausanne, Lausanne, Switzerland, and Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland. [3] Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Martin Eisenacher
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Gerhard Mayer
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Laurent Gatto
- Computational Proteomics Unit and Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Alex Campos
- Integromics SL, Santiago Grisolia, Madrid, Spain
| | - Robert J Chalkley
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | | | - Juan Pablo Albar
- ProteoRed-ISCIII, National Center for Biotechnology-CSIC, Madrid, Spain
| | | | - Rolf Apweiler
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Gilbert S Omenn
- 1] Institute for Systems Biology, Seattle, Washington, USA. [2] Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Lennart Martens
- 1] Department of Medical Protein Research, VIB, Ghent, Belgium. [2] Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Andrew R Jones
- Institute of Integrative Biology, University of Liverpool, UK
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBLEBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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49
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Abstract
In large-scale proteomic experiments, multiple peptide precursors are often cofragmented simultaneously in the same mixture tandem mass (MS/MS) spectrum. These spectra tend to elude current computational tools because of the ubiquitous assumption that each spectrum is generated from only one peptide. Therefore, tools that consider multiple peptide matches to each MS/MS spectrum can potentially improve the relatively low spectrum identification rate often observed in proteomics experiments. More importantly, data independent acquisition protocols promoting the cofragmentation of multiple precursors are emerging as alternative methods that can greatly improve the throughput of peptide identifications but their success also depends on the availability of algorithms to identify multiple peptides from each MS/MS spectrum. Here we address a fundamental question in the identification of mixture MS/MS spectra: determining the statistical significance of multiple peptides matched to a given MS/MS spectrum. We propose the MixGF generating function model to rigorously compute the statistical significance of peptide identifications for mixture spectra and show that this approach improves the sensitivity of current mixture spectra database search tools by a ≈30-390%. Analysis of multiple data sets with MixGF reveals that in complex biological samples the number of identified mixture spectra can be as high as 20% of all the identified spectra and the number of unique peptides identified only in mixture spectra can be up to 35.4% of those identified in single-peptide spectra.
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Affiliation(s)
- Jian Wang
- From the ‡Bioinformatics Program, University of California, San Diego, La Jolla, California
| | - Philip E Bourne
- §Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California
| | - Nuno Bandeira
- §Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California; ¶Center for Computational Mass Spectrometry, University of California, San Diego, La, Jolla, California; ‖Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92092
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50
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Mohimani H, Kersten RD, Liu WT, Wang M, Purvine SO, Wu S, Brewer HM, Pasa-Tolic L, Bandeira N, Moore BS, Pevzner PA, Dorrestein PC. Automated genome mining of ribosomal peptide natural products. ACS Chem Biol 2014; 9:1545-51. [PMID: 24802639 PMCID: PMC4215869 DOI: 10.1021/cb500199h] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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Ribosomally synthesized and posttranslationally
modified peptides
(RiPPs), especially from microbial sources, are a large group of bioactive
natural products that are a promising source of new (bio)chemistry
and bioactivity.1 In light of exponentially
increasing microbial genome databases and improved mass spectrometry
(MS)-based metabolomic platforms, there is a need for computational
tools that connect natural product genotypes predicted from microbial
genome sequences with their corresponding chemotypes from metabolomic
data sets. Here, we introduce RiPPquest, a tandem mass spectrometry
database search tool for identification of microbial RiPPs, and apply
it to lanthipeptide discovery. RiPPquest uses genomics to limit search
space to the vicinity of RiPP biosynthetic genes and proteomics to
analyze extensive peptide modifications and compute p-values of peptide-spectrum
matches (PSMs). We highlight RiPPquest by connecting multiple RiPPs
from extracts of Streptomyces to their gene clusters
and by the discovery of a new class III lanthipeptide, informatipeptin,
from Streptomyces viridochromogenes DSM 40736 to
reflect that it is a natural product that was discovered by mass spectrometry
based genome mining using algorithmic tools rather than manual inspection
of mass spectrometry data and genetic information. The presented tool
is available at cyclo.ucsd.edu.
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Affiliation(s)
- Hosein Mohimani
- Department
of Electrical and Computer Engineering, University of California San Diego, La Jolla, California 92093, United States
| | - Roland D. Kersten
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Wei-Ting Liu
- Department
of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Mingxun Wang
- Department
of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
| | - Samuel O. Purvine
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Si Wu
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Heather M. Brewer
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ljiljana Pasa-Tolic
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Nuno Bandeira
- Department
of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
- Skaggs School
of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Bradley S. Moore
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
- Skaggs School
of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Pavel A. Pevzner
- Department
of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
| | - Pieter C. Dorrestein
- Department
of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
- Skaggs School
of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
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