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Baker MS, Ahn SB, Mohamedali A, Islam MT, Cantor D, Verhaert PD, Fanayan S, Sharma S, Nice EC, Connor M, Ranganathan S. Accelerating the search for the missing proteins in the human proteome. Nat Commun 2017; 8:14271. [PMID: 28117396 PMCID: PMC5286205 DOI: 10.1038/ncomms14271] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 12/06/2016] [Indexed: 12/25/2022] Open
Abstract
The Human Proteome Project (HPP) aims to discover high-stringency data for all proteins encoded by the human genome. Currently, ∼18% of the proteins in the human proteome (the missing proteins) do not have high-stringency evidence (for example, mass spectrometry) confirming their existence, while much additional information is available about many of these missing proteins. Here, we present MissingProteinPedia as a community resource to accelerate the discovery and understanding of these missing proteins. The Human Proteome Project aims to catalogue the ∼20,000 proteins encoded by the human genome. In this review, Baker et al . focus on the missing proteins, proteins that lack high stringency proteomic evidence, and launch MissingProteinPedia, a database aimed at accelerating the search for missing proteins.
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Affiliation(s)
- Mark S. Baker
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, New South Wales 2109, Australia
| | - Seong Beom Ahn
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, New South Wales 2109, Australia
| | - Abidali Mohamedali
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, New South Wales 2109, Australia
- Department of Chemistry & Biomolecular Sciences, Macquarie University, New South Wales 2109, Australia
| | - Mohammad T. Islam
- Department of Chemistry & Biomolecular Sciences, Macquarie University, New South Wales 2109, Australia
| | - David Cantor
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, New South Wales 2109, Australia
| | | | - Susan Fanayan
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, New South Wales 2109, Australia
| | - Samridhi Sharma
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, New South Wales 2109, Australia
| | - Edouard C. Nice
- Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Mark Connor
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, New South Wales 2109, Australia
| | - Shoba Ranganathan
- Department of Chemistry & Biomolecular Sciences, Macquarie University, New South Wales 2109, Australia
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Islam MT, Mohamedali A, Ahn SB, Nawar I, Baker MS, Ranganathan S. A Systematic Bioinformatics Approach to Identify High Quality Mass Spectrometry Data and Functionally Annotate Proteins and Proteomes. Methods Mol Biol 2017; 1549:163-176. [PMID: 27975291 DOI: 10.1007/978-1-4939-6740-7_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In the past decade, proteomics and mass spectrometry have taken tremendous strides forward, particularly in the life sciences, spurred on by rapid advances in technology resulting in generation and conglomeration of vast amounts of data. Though this has led to tremendous advancements in biology, the interpretation of the data poses serious challenges for many practitioners due to the immense size and complexity of the data. Furthermore, the lack of annotation means that a potential gold mine of relevant biological information may be hiding within this data. We present here a simple and intuitive workflow for the research community to investigate and mine this data, not only to extract relevant data but also to segregate usable, quality data to develop hypotheses for investigation and validation. We apply an MS evidence workflow for verifying peptides of proteins from one's own data as well as publicly available databases. We then integrate a suite of freely available bioinformatics analysis and annotation software tools to identify homologues and map putative functional signatures, gene ontology and biochemical pathways. We also provide an example of the functional annotation of missing proteins in human chromosome 7 data from the NeXtProt database, where no evidence is available at the proteomic, antibody, or structural levels. We give examples of protocols, tools and detailed flowcharts that can be extended or tailored to interpret and annotate the proteome of any novel organism.
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Affiliation(s)
- Mohammad Tawhidul Islam
- Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia
| | - Abidali Mohamedali
- Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia.,Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Seong Beom Ahn
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Ishmam Nawar
- Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Shoba Ranganathan
- Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia.
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3
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Islam MT, Mohamedali A, Fernandes CS, Baker MS, Ranganathan S. De Novo Peptide Sequencing: Deep Mining of High-Resolution Mass Spectrometry Data. Methods Mol Biol 2017; 1549:119-134. [PMID: 27975288 DOI: 10.1007/978-1-4939-6740-7_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
High resolution mass spectrometry has revolutionized proteomics over the past decade, resulting in tremendous amounts of data in the form of mass spectra, being generated in a relatively short span of time. The mining of this spectral data for analysis and interpretation though has lagged behind such that potentially valuable data is being overlooked because it does not fit into the mold of traditional database searching methodologies. Although the analysis of spectra by de novo sequences removes such biases and has been available for a long period of time, its uptake has been slow or almost nonexistent within the scientific community. In this chapter, we propose a methodology to integrate de novo peptide sequencing using three commonly available software solutions in tandem, complemented by homology searching, and manual validation of spectra. This simplified method would allow greater use of de novo sequencing approaches and potentially greatly increase proteome coverage leading to the unearthing of valuable insights into protein biology, especially of organisms whose genomes have been recently sequenced or are poorly annotated.
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Affiliation(s)
- Mohammad Tawhidul Islam
- Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia
| | - Abidali Mohamedali
- Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Criselda Santan Fernandes
- Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Shoba Ranganathan
- Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia.
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Segura V, Garin-Muga A, Guruceaga E, Corrales FJ. Progress and pitfalls in finding the 'missing proteins' from the human proteome map. Expert Rev Proteomics 2016; 14:9-14. [PMID: 27885863 DOI: 10.1080/14789450.2017.1265450] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
INTRODUCTION The Human Proteome Project was launched with two main goals: the comprehensive and systematic definition of the human proteome map and the development of ready to use analytical tools to measure relevant proteins in their biological context in health and disease. Despite the great progress in this endeavour, there is still a group of reluctant proteins with no, or scarce, experimental evidence supporting their existence. These are called the 'missing proteins' and represent one of the biggest challenges to complete the human proteome map. Areas covered: This review focuses on the description of the missing proteome based on the HUPO standards, the analysis of the reasons explaining the difficulty of detecting missing proteins and the strategies currently used in the search for missing proteins. The present and future of the quest for the missing proteins is critically revised hereafter. Expert commentary: An overarching multidisciplinary effort is currently being done under the HUPO umbrella to allow completion of the human proteome map. It is expected that the detection of missing proteins will grow in the coming years since the methods and the best tissue/cell type sample for their search are already on the table.
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Affiliation(s)
- Victor Segura
- a Proteomics and Bioinformatics Laboratory, CIMA , University of Navarra , Pamplona , Spain
| | - Alba Garin-Muga
- a Proteomics and Bioinformatics Laboratory, CIMA , University of Navarra , Pamplona , Spain
| | - Elizabeth Guruceaga
- a Proteomics and Bioinformatics Laboratory, CIMA , University of Navarra , Pamplona , Spain
| | - Fernando J Corrales
- a Proteomics and Bioinformatics Laboratory, CIMA , University of Navarra , Pamplona , Spain
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Locard-Paulet M, Pible O, Gonzalez de Peredo A, Alpha-Bazin B, Almunia C, Burlet-Schiltz O, Armengaud J. Clinical implications of recent advances in proteogenomics. Expert Rev Proteomics 2016; 13:185-99. [DOI: 10.1586/14789450.2016.1132169] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Kumar D, Jain A, Dash D. Probing the Missing Human Proteome: A Computational Perspective. J Proteome Res 2015; 14:4949-58. [DOI: 10.1021/acs.jproteome.5b00728] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Dhirendra Kumar
- G. N. Ramachandran Knowledge
Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, Mathura Road, Delhi 110025, India
| | - Aradhya Jain
- G. N. Ramachandran Knowledge
Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, Mathura Road, Delhi 110025, India
| | - Debasis Dash
- G. N. Ramachandran Knowledge
Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, Mathura Road, Delhi 110025, India
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7
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Horvatovich P, Lundberg EK, Chen YJ, Sung TY, He F, Nice EC, Goode RJ, Yu S, Ranganathan S, Baker MS, Domont GB, Velasquez E, Li D, Liu S, Wang Q, He QY, Menon R, Guan Y, Corrales FJ, Segura V, Casal JI, Pascual-Montano A, Albar JP, Fuentes M, Gonzalez-Gonzalez M, Diez P, Ibarrola N, Degano RM, Mohammed Y, Borchers CH, Urbani A, Soggiu A, Yamamoto T, Salekdeh GH, Archakov A, Ponomarenko E, Lisitsa A, Lichti CF, Mostovenko E, Kroes RA, Rezeli M, Végvári Á, Fehniger TE, Bischoff R, Vizcaíno JA, Deutsch EW, Lane L, Nilsson CL, Marko-Varga G, Omenn GS, Jeong SK, Lim JS, Paik YK, Hancock WS. Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project. J Proteome Res 2015; 14:3415-31. [DOI: 10.1021/pr5013009] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Péter Horvatovich
- Analytical
Biochemistry, Department of Pharmacy, University of Groningen, A. Deusinglaan
1, 9713 AV Groningen, The Netherlands
| | - Emma K. Lundberg
- Science
for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Yu-Ju Chen
- Institute
of Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Taipei 115, Taiwan
| | - Ting-Yi Sung
- Institute
of Information Science, Academia Sinica, 128 Academia Road Sec. 2, Taipei 115, Taiwan
| | - Fuchu He
- The State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, No. 27 Taiping Road, Haidian District, Beijing 100850, China
| | - Edouard C. Nice
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Robert J. Goode
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Simon Yu
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Shoba Ranganathan
- Department
of Chemistry and Biomolecular Sciences and ARC Centre of Excellence
in Bioinformatics, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Mark S. Baker
- Australian
School of Advanced Medicine, Macquarie University, Sydney, NSW 2109, Australia
| | - Gilberto B. Domont
- Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, Cidade Universitária, Av Athos da Silveira Ramos 149, CT-A542, 21941-909 Rio de Janeriro, Rj, Brazil
| | - Erika Velasquez
- Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, Cidade Universitária, Av Athos da Silveira Ramos 149, CT-A542, 21941-909 Rio de Janeriro, Rj, Brazil
| | - Dong Li
- The State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, No. 27 Taiping Road, Haidian District, Beijing 100850, China
| | - Siqi Liu
- Beijing Institute of Genomics and BGI Shenzhen, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China
- BGI Shenzhen, Beishan Road, Yantian District, Shenzhen, 518083, China
| | - Quanhui Wang
- Beijing Institute of Genomics and BGI Shenzhen, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Qing-Yu He
- Key Laboratory of Functional Protein
Research of Guangdong
Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Rajasree Menon
- Department of Computational Medicine & Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
| | - Yuanfang Guan
- Departments of Computational Medicine & Bioinformatics and Computer Sciences, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
| | - Fernando J. Corrales
- ProteoRed-ISCIII,
Biomolecular and Bioinformatics Resources Platform (PRB2), Spanish
Consortium of C-HPP (Chr-16), CIMA, University of Navarra, 31008 Pamplona, Spain
- Chr16 SpHPP Consortium, CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Victor Segura
- ProteoRed-ISCIII,
Biomolecular and Bioinformatics Resources Platform (PRB2), Spanish
Consortium of C-HPP (Chr-16), CIMA, University of Navarra, 31008 Pamplona, Spain
- Chr16 SpHPP Consortium, CIMA, University of Navarra, 31008 Pamplona, Spain
| | - J. Ignacio Casal
- Department
of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CIB-CSIC), 28040 Madrid, Spain
| | | | - Juan P. Albar
- Centro Nacional de Biotecnologia (CNB-CSIC), Cantoblanco, 28049 Madrid, Spain
| | - Manuel Fuentes
- Cancer
Research Center. Proteomics Unit and General Service of Cytometry,
Department of Medicine, University of Salmanca-CSIC, IBSAL, Campus Miguel de Unamuno
s/n, 37007 Salamanca, Spain
| | - Maria Gonzalez-Gonzalez
- Cancer
Research Center. Proteomics Unit and General Service of Cytometry,
Department of Medicine, University of Salmanca-CSIC, IBSAL, Campus Miguel de Unamuno
s/n, 37007 Salamanca, Spain
| | - Paula Diez
- Cancer
Research Center. Proteomics Unit and General Service of Cytometry,
Department of Medicine, University of Salmanca-CSIC, IBSAL, Campus Miguel de Unamuno
s/n, 37007 Salamanca, Spain
| | - Nieves Ibarrola
- Cancer
Research Center. Proteomics Unit and General Service of Cytometry,
Department of Medicine, University of Salmanca-CSIC, IBSAL, Campus Miguel de Unamuno
s/n, 37007 Salamanca, Spain
| | - Rosa M. Degano
- Cancer
Research Center. Proteomics Unit and General Service of Cytometry,
Department of Medicine, University of Salmanca-CSIC, IBSAL, Campus Miguel de Unamuno
s/n, 37007 Salamanca, Spain
| | - Yassene Mohammed
- University of Victoria-Genome British Columbia Proteomics
Centre, Vancouver Island
Technology Park, #3101−4464 Markham Street, Victoria, British Columbia V8Z 7X8, Canada
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Christoph H. Borchers
- University of Victoria-Genome British Columbia Proteomics
Centre, Vancouver Island
Technology Park, #3101−4464 Markham Street, Victoria, British Columbia V8Z 7X8, Canada
| | - Andrea Urbani
- Proteomics
and Metabonomic, Laboratory, Fondazione Santa Lucia, Rome, Italy
- Department
of Experimental Medicine and Surgery, University of Rome “Tor Vergata”, Rome, Italy
| | - Alessio Soggiu
- Department
of Veterinary Science and Public Health (DIVET), University of Milano, via Celoria 10, 20133 Milano, Italy
| | - Tadashi Yamamoto
- Institute
of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran
| | | | | | - Andrey Lisitsa
- Orechovich Institute of Biomedical Chemistry, Moscow, Russia
| | - Cheryl F. Lichti
- Department
of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas 77555-0617, United States
| | - Ekaterina Mostovenko
- Department
of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas 77555-0617, United States
| | - Roger A. Kroes
- Falk Center for Molecular Therapeutics, Department of Biomedical Engineering, Northwestern University, 1801 Maple Ave., Suite 4300, Evanston, Illinois 60201, United States
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
| | - Ákos Végvári
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
| | - Thomas E. Fehniger
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
| | - Rainer Bischoff
- Analytical
Biochemistry, Department of Pharmacy, University of Groningen, A. Deusinglaan
1, 9713 AV Groningen, The Netherlands
| | - Juan Antonio Vizcaíno
- European Molecular
Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, United Kingdom
| | - Eric W. Deutsch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States
| | - Lydie Lane
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
- Department
of Human Protein Science, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Carol L. Nilsson
- Department
of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas 77555-0617, United States
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
| | - Gilbert S. Omenn
- Departments of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics and School of Public Health, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
| | - Seul-Ki Jeong
- Departments of Integrated Omics for Biomedical Science & Biochemistry, College of Life Science and Technology, Yonsei Proteome Research Center, Yonsei University, Seoul, 120-749, Korea
| | - Jong-Sun Lim
- Departments of Integrated Omics for Biomedical Science & Biochemistry, College of Life Science and Technology, Yonsei Proteome Research Center, Yonsei University, Seoul, 120-749, Korea
| | - Young-Ki Paik
- Departments of Integrated Omics for Biomedical Science & Biochemistry, College of Life Science and Technology, Yonsei Proteome Research Center, Yonsei University, Seoul, 120-749, Korea
| | - William S. Hancock
- The
Barnett Institute of Chemical and Biological Analysis, Northeastern University, 140 The Fenway, Boston, Massachusetts 02115, United States
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8
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Chen Y, Li Y, Zhong J, Zhang J, Chen Z, Yang L, Cao X, He QY, Zhang G, Wang T. Identification of Missing Proteins Defined by Chromosome-Centric Proteome Project in the Cytoplasmic Detergent-Insoluble Proteins. J Proteome Res 2015; 14:3693-709. [DOI: 10.1021/pr501103r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yang Chen
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yaxing Li
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Jiayong Zhong
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Jing Zhang
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zhipeng Chen
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Lijuan Yang
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xin Cao
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Qing-Yu He
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Gong Zhang
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Tong Wang
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
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9
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Reddy PJ, Ray S, Srivastava S. The Quest of the Human Proteome and the Missing Proteins: Digging Deeper. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:276-82. [DOI: 10.1089/omi.2015.0035] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Panga Jaipal Reddy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sandipan Ray
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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10
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Paik YK, Omenn GS, Thongboonkerd V, Marko-Varga G, Hancock WS. Genome-wide proteomics, Chromosome-Centric Human Proteome Project (C-HPP), part II. J Proteome Res 2013; 13:1-4. [PMID: 24328071 DOI: 10.1021/pr4011958] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Young-Ki Paik
- Yonsei Proteome Research Center, Departments of Integrated Omics for Biomedical Science and Biochemistry, Yonsei University , 50 Yonsei-ro, Sudaemoon-ku, Seoul 120-749, Korea
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11
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Islam MT, Garg G, Hancock WS, Risk BA, Baker MS, Ranganathan S. Protannotator: A Semiautomated Pipeline for Chromosome-Wise Functional Annotation of the “Missing” Human Proteome. J Proteome Res 2013; 13:76-83. [DOI: 10.1021/pr400794x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | | | - William S. Hancock
- Barnett
Institute, Northeastern University, 140 The Fenway, Boston, Massachusetts 02115, United States
| | - Brian A. Risk
- College
of Arts and Sciences, Boise State University, 1910 University Drive, Boise, Idaho 83725, United States
| | | | - Shoba Ranganathan
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, 117599 Singapore
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12
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Zhong J, Cui Y, Guo J, Chen Z, Yang L, He QY, Zhang G, Wang T. Resolving chromosome-centric human proteome with translating mRNA analysis: a strategic demonstration. J Proteome Res 2013; 13:50-9. [PMID: 24200226 DOI: 10.1021/pr4007409] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chromosome-centric human proteome project (C-HPP) aims at differentiating chromosome-based and tissue-specific protein compositions in terms of protein expression, quantification, and modification. We previously found that the analysis of translating mRNA (mRNA attached to ribosome-nascent chain complex, RNC-mRNA) can explain over 94% of mRNA-protein abundance. Therefore, we propose here to use full-length RNC-mRNA information to illustrate protein expression both qualitatively and quantitatively. We performed RNA-seq on RNC-mRNA (RNC-seq) and detected 12,758 and 14,113 translating genes in human normal bronchial epithelial (HBE) cells and human colorectal adenocarcinoma Caco-2 cells, respectively. We found that most of these genes were mapped with >80% of coding sequence coverage. In Caco-2 cells, we provided translating evidence on 4180 significant single-nucleotide variations. While using RNC-mRNA data as a standard for proteomic data integration, both translating and protein evidence of 7876 genes can be acquired from four interlaboratory data sets with different MS platforms. In addition, we detected 1397 noncoding mRNAs that were attached to ribosomes, suggesting a potential source of new protein explorations. By comparing the two cell lines, a total of 677 differentially translated genes were found to be nonevenly distributed across chromosomes. In addition, 2105 genes in Caco-2 and 750 genes in HBE cells are expressed in a cell-specific manner. These genes are significantly and specifically clustered on multiple chromosomes, such as chromosome 19. We conclude that HPP/C-HPP investigations can be considerably improved by integrating RNC-mRNA analysis with MS, bioinformatics, and antibody-based verifications.
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Affiliation(s)
- Jiayong Zhong
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , 601 Huangpu Avenue West, Guangzhou 510632, China
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Islam MT, Mohamedali A, Garg G, Khan JM, Gorse AD, Parsons J, Marshall P, Ranganathan S, Baker MS. Unlocking the puzzling biology of the black Périgord truffle Tuber melanosporum. J Proteome Res 2013; 12:5349-56. [PMID: 24147936 DOI: 10.1021/pr400650c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The black Périgord truffle (Tuber melanosporum Vittad.) is a highly prized food today, with its unique scent (i.e., perfume) and texture. Despite these attributes, it remains relatively poorly studied, lacking "omics" information to characterize its biology and biochemistry, especially changes associated with freshness and the proteins/metabolites responsible for its organoleptic properties. In this study, we have functionally annotated the truffle proteome from the 2010 T. melanosporum genome comprising 12,771 putative nonredundant proteins. Using sequential BLAST search strategies, we identified homologues for 2587 proteins with 2486 (96.0%) fungal homologues (available from http://biolinfo.org/protannotator/blacktruffle.php). A combined 1D PAGE and high-accuracy LC-MS/MS proteomic study was employed to validate the results of the functional annotation and identified 836 (6.5%) proteins, of which 47.5% (i.e., 397) were present in our bioinformatics studies. Our study, functionally annotating 6487 black Périgord truffle proteins and confirming 836 by proteomic experiments, is by far the most comprehensive study to date contributing significantly to the scientific community. This study has resulted in the functional characterization of novel proteins to increase our biological understanding of this organism and to uncover potential biomarkers of authenticity, freshness, and perfume maturation.
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Affiliation(s)
- Mohammad Tawhidul Islam
- Department of Chemistry and Biomolecular Sciences, Macquarie University , NSW 2109, Australia
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