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Ni Z, Wölk M, Jukes G, Mendivelso Espinosa K, Ahrends R, Aimo L, Alvarez-Jarreta J, Andrews S, Andrews R, Bridge A, Clair GC, Conroy MJ, Fahy E, Gaud C, Goracci L, Hartler J, Hoffmann N, Kopczyinki D, Korf A, Lopez-Clavijo AF, Malik A, Ackerman JM, Molenaar MR, O'Donovan C, Pluskal T, Shevchenko A, Slenter D, Siuzdak G, Kutmon M, Tsugawa H, Willighagen EL, Xia J, O'Donnell VB, Fedorova M. Guiding the choice of informatics software and tools for lipidomics research applications. Nat Methods 2023; 20:193-204. [PMID: 36543939 PMCID: PMC10263382 DOI: 10.1038/s41592-022-01710-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [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: 05/24/2022] [Accepted: 11/02/2022] [Indexed: 12/24/2022]
Abstract
Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across biology and biomedicine. These generate extremely large raw datasets requiring sophisticated solutions to support automated data processing. To address this, numerous software tools have been developed and tailored for specific tasks. However, for researchers, deciding which approach best suits their application relies on ad hoc testing, which is inefficient and time consuming. Here we first review the data processing pipeline, summarizing the scope of available tools. Next, to support researchers, LIPID MAPS provides an interactive online portal listing open-access tools with a graphical user interface. This guides users towards appropriate solutions within major areas in data processing, including (1) lipid-oriented databases, (2) mass spectrometry data repositories, (3) analysis of targeted lipidomics datasets, (4) lipid identification and (5) quantification from untargeted lipidomics datasets, (6) statistical analysis and visualization, and (7) data integration solutions. Detailed descriptions of functions and requirements are provided to guide customized data analysis workflows.
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Affiliation(s)
- Zhixu Ni
- Center of Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany
| | - Michele Wölk
- Center of Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany
| | - Geoff Jukes
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | | | - Robert Ahrends
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Lucila Aimo
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland
| | - Jorge Alvarez-Jarreta
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Simon Andrews
- Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Robert Andrews
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Alan Bridge
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland
| | - Geremy C Clair
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Matthew J Conroy
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Eoin Fahy
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Caroline Gaud
- Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Jürgen Hartler
- Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria
- Field of Excellence BioHealthe-University of Graz, Graz, Austria
| | - Nils Hoffmann
- Center for Biotechnology, University of Bielefeld, Bielefeld, Germany
| | - Dominik Kopczyinki
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Ansgar Korf
- Bruker Daltonics GmbH & Co. KG, Bremen, Germany
| | | | - Adnan Malik
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Martijn R Molenaar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Claire O'Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Tomáš Pluskal
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Denise Slenter
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Gary Siuzdak
- Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, CA, USA
| | - Martina Kutmon
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
- Maastricht Centre for Systems Biology, Maastricht University, Maastricht, The Netherlands
| | - Hiroshi Tsugawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Egon L Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Montreal, Canada
| | - Valerie B O'Donnell
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK.
| | - Maria Fedorova
- Center of Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany.
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2
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Hohenwallner K, Troppmair N, Panzenboeck L, Kasper C, El Abiead Y, Koellensperger G, Lamp LM, Hartler J, Egger D, Rampler E. Decoding Distinct Ganglioside Patterns of Native and Differentiated Mesenchymal Stem Cells by a Novel Glycolipidomics Profiling Strategy. JACS Au 2022; 2:2466-2480. [PMID: 36465531 PMCID: PMC9709940 DOI: 10.1021/jacsau.2c00230] [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] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 10/01/2022] [Accepted: 10/03/2022] [Indexed: 06/17/2023]
Abstract
Gangliosides are an indispensable glycolipid class concentrated on cell surfaces with a critical role in stem cell differentiation. Nonetheless, owing to the lack of suitable methods for scalable analysis covering the full scope of ganglioside molecular diversity, their mechanistic properties in signaling and differentiation remain undiscovered to a large extent. This work introduces a sensitive and comprehensive ganglioside assay based on liquid chromatography, high-resolution mass spectrometry, and multistage fragmentation. Complemented by an open-source data evaluation workflow, we provide automated in-depth lipid species-level and molecular species-level annotation based on decision rule sets for all major ganglioside classes. Compared to conventional state-of-the-art methods, the presented ganglioside assay offers (1) increased sensitivity, (2) superior structural elucidation, and (3) the possibility to detect novel ganglioside species. A major reason for the highly improved sensitivity is the optimized spectral readout based on the unique capability of two parallelizable mass analyzers for multistage fragmentation. We demonstrated the high-throughput universal capability of our novel analytical strategy by identifying 254 ganglioside species. As a proof of concept, 137 unique gangliosides were annotated in native and differentiated human mesenchymal stem cells including 78 potential cell-state-specific markers and 38 previously unreported gangliosides. A general increase of the ganglioside numbers upon differentiation was observed as well as cell-state-specific clustering based on the ganglioside species patterns. The combination of the developed glycolipidomics assay with the extended automated annotation tool enables comprehensive in-depth ganglioside characterization as shown on biological samples of interest. Our results suggest ganglioside patterns as a promising quality control tool for stem cells and their differentiation products. Additionally, we believe that our analytical workflow paves the way for probing glycolipid-based biochemical processes shedding light on the enigmatic processes of gangliosides and glycolipids in general.
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Affiliation(s)
- Katharina Hohenwallner
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Vienna
Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna 1090, Austria
| | - Nina Troppmair
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Vienna
Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna 1090, Austria
| | - Lisa Panzenboeck
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Vienna
Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna 1090, Austria
| | - Cornelia Kasper
- Institute
of Cell and Tissue Culture Technologies, University of Natural Resources and Life Sciences, Vienna 1190, Austria
| | - Yasin El Abiead
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
| | - Gunda Koellensperger
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
| | - Leonida M. Lamp
- Institute
of Pharmaceutical Sciences, University of
Graz, Graz 8010, Austria
| | - Jürgen Hartler
- Institute
of Pharmaceutical Sciences, University of
Graz, Graz 8010, Austria
- Field
of Excellence BioHealth − University
of Graz, Graz 8010, Austria
| | - Dominik Egger
- Institute
of Cell and Tissue Culture Technologies, University of Natural Resources and Life Sciences, Vienna 1190, Austria
| | - Evelyn Rampler
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
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3
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McDonald JG, Ejsing CS, Kopczynski D, Holčapek M, Aoki J, Arita M, Arita M, Baker ES, Bertrand-Michel J, Bowden JA, Brügger B, Ellis SR, Fedorova M, Griffiths WJ, Han X, Hartler J, Hoffmann N, Koelmel JP, Köfeler HC, Mitchell TW, O'Donnell VB, Saigusa D, Schwudke D, Shevchenko A, Ulmer CZ, Wenk MR, Witting M, Wolrab D, Xia Y, Ahrends R, Liebisch G, Ekroos K. Introducing the Lipidomics Minimal Reporting Checklist. Nat Metab 2022; 4:1086-1088. [PMID: 35934691 DOI: 10.1038/s42255-022-00628-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jeffrey G McDonald
- Center for Human Nutrition and Department of Molecular Genetics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Dominik Kopczynski
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Michal Holčapek
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic
| | - Junken Aoki
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan
| | - Makoto Arita
- RIKEN, Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
| | - Justine Bertrand-Michel
- MetaboHUB-Metatoul, National Infrastructure of Metabolomics and Fluxomics, Inserm I2MC, Toulouse, France
| | - John A Bowden
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Shane R Ellis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
- Illawarra Heath and Medical Research Institute, Wollongong, New South Wales, Australia
| | - Maria Fedorova
- Center for Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany
| | | | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Department of Medicine - Diabetes, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Jürgen Hartler
- Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Nils Hoffmann
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jeremy P Koelmel
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Harald C Köfeler
- Core Facility Mass Spectrometry and Lipidomics, ZMF, Medical University of Graz, Graz, Austria
| | - Todd W Mitchell
- Illawarra Heath and Medical Research Institute, Wollongong, New South Wales, Australia
| | - Valerie B O'Donnell
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Dominik Schwudke
- Research Center Borstel - Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Thematic Translational Unit Tuberculosis, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Andrej Shevchenko
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Candice Z Ulmer
- Office of Public Health Science, Food Safety and Inspection Service, US Department of Agriculture, Athens, GA, USA
| | - Markus R Wenk
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, Singapore
| | - Michael Witting
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Neuherberg, Germany
| | - Denise Wolrab
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic
| | - Yu Xia
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Robert Ahrends
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg, Germany.
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Esbo, Finland.
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4
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Vigor C, Züllig T, Eichmann TO, Oger C, Zhou B, Rechberger GN, Hilsberg L, Trötzmüller M, Pellegrino RM, Alabed HBR, Hartler J, Wolinski H, Galano JM, Durand T, Spener F. α-Linolenic acid and product octadecanoids in Styrian pumpkin seeds and oils: How processing impacts lipidomes of fatty acid, triacylglycerol and oxylipin molecular structures. Food Chem 2022; 371:131194. [PMID: 34600364 DOI: 10.1016/j.foodchem.2021.131194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 09/06/2021] [Accepted: 09/16/2021] [Indexed: 12/13/2022]
Abstract
Styrian pumpkin seed oil is a conditioned green-colored oil renowned for nutty smell and taste. Due to α-linolenic acid (ALA) contents below 1% of total fatty acids and the prospect of nutritional health claims based on its potential oxidation products, we investigated the fate of ALA and product oxylipins in the course of down-stream processing of seeds and in oils. Lipidomic analyses with Lipid Data Analyzer 2.8.1 revealed: Processing did not change (1) main fatty acid composition in the oils, (2) amounts of triacylglycerol species, (3) structures of triacylglycerol molecular species containing ALA. (4) Minor precursor ALA in fresh Styrian and normal pumpkins produced 6 product phytoprostanes in either cultivar, quantitatively more in the latter. (5) In oil samples 7 phytoprostanes and 2 phytofurans were detected. The latter two are specific for their presence in pumpkin seed oils, of note, quantitatively more in conditioned oils than in cold-pressed native oils.
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Affiliation(s)
- Claire Vigor
- Institute of Biomolecules Max Mousseron, UMR 5247, CNRS, University of Montpellier, ENSCM, 34093 Montpellier, France
| | - Thomas Züllig
- Core Facility Mass Spectrometry, Medical University of Graz, Stiftingtalstr. 24, 8010 Graz, Austria
| | - Thomas O Eichmann
- Department of Molecular Biosciences, University of Graz, Heinrichstr. 31/II, 8010 Graz, Austria
| | - Camille Oger
- Institute of Biomolecules Max Mousseron, UMR 5247, CNRS, University of Montpellier, ENSCM, 34093 Montpellier, France
| | - Bingqing Zhou
- Institute of Biomolecules Max Mousseron, UMR 5247, CNRS, University of Montpellier, ENSCM, 34093 Montpellier, France
| | - Gerald N Rechberger
- Department of Molecular Biosciences, University of Graz, Heinrichstr. 31/II, 8010 Graz, Austria
| | | | - Martin Trötzmüller
- Core Facility Mass Spectrometry, Medical University of Graz, Stiftingtalstr. 24, 8010 Graz, Austria
| | - Roberto M Pellegrino
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via del Giochetto, Building B, 06126 Perugia, Italy
| | - Husam B R Alabed
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via del Giochetto, Building B, 06126 Perugia, Italy
| | - Jürgen Hartler
- Institute of Pharmaceutical Sciences, University of Graz, Universitätsplatz 1/I, 8010 Graz, Austria; Field of Excellence BioHealth - University of Graz, Humboldtstraße 50, 8010 Graz, Austria
| | - Heimo Wolinski
- Department of Molecular Biosciences, University of Graz, Heinrichstr. 31/II, 8010 Graz, Austria
| | - Jean-Marie Galano
- Institute of Biomolecules Max Mousseron, UMR 5247, CNRS, University of Montpellier, ENSCM, 34093 Montpellier, France
| | - Thierry Durand
- Institute of Biomolecules Max Mousseron, UMR 5247, CNRS, University of Montpellier, ENSCM, 34093 Montpellier, France
| | - Friedrich Spener
- Department of Molecular Biosciences, University of Graz, Heinrichstr. 31/II, 8010 Graz, Austria; Division of Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Neue Stiftingtalstr. 6/6, 8010 Graz, Austria.
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5
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Vvedenskaya O, Rose TD, Knittelfelder O, Palladini A, Wodke JAH, Schuhmann K, Ackerman JM, Wang Y, Has C, Brosch M, Thangapandi VR, Buch S, Züllig T, Hartler J, Köfeler HC, Röcken C, Coskun Ü, Klipp E, von Schoenfels W, Gross J, Schafmayer C, Hampe J, Pauling JK, Shevchenko A. Nonalcoholic fatty liver disease stratification by liver lipidomics. J Lipid Res 2021; 62:100104. [PMID: 34384788 PMCID: PMC8488246 DOI: 10.1016/j.jlr.2021.100104] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/20/2021] [Accepted: 07/30/2021] [Indexed: 02/06/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a common metabolic dysfunction leading to hepatic steatosis. However, NAFLD's global impact on the liver lipidome is poorly understood. Using high-resolution shotgun mass spectrometry, we quantified the molar abundance of 316 species from 22 major lipid classes in liver biopsies of 365 patients, including nonsteatotic patients with normal or excessive weight, patients diagnosed with NAFL (nonalcoholic fatty liver) or NASH (nonalcoholic steatohepatitis), and patients bearing common mutations of NAFLD-related protein factors. We confirmed the progressive accumulation of di- and triacylglycerols and cholesteryl esters in the liver of NAFL and NASH patients, while the bulk composition of glycerophospho- and sphingolipids remained unchanged. Further stratification by biclustering analysis identified sphingomyelin species comprising n24:2 fatty acid moieties as membrane lipid markers of NAFLD. Normalized relative abundance of sphingomyelins SM 43:3;2 and SM 43:1;2 containing n24:2 and n24:0 fatty acid moieties, respectively, showed opposite trends during NAFLD progression and distinguished NAFL and NASH lipidomes from the lipidome of nonsteatotic livers. Together with several glycerophospholipids containing a C22:6 fatty acid moiety, these lipids serve as markers of early and advanced stages of NAFL.
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Affiliation(s)
- Olga Vvedenskaya
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Tim Daniel Rose
- LipiTUM, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Oskar Knittelfelder
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Alessandra Palladini
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum Munich at the University Hospital Carl Gustav Carus, Technische Universität (TU) Dresden, Dresden, Germany; German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | | | - Kai Schuhmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Yuting Wang
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Canan Has
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Mario Brosch
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Germany; Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Veera Raghavan Thangapandi
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Germany; Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Stephan Buch
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Germany; Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Thomas Züllig
- Core Facility Mass Spectrometry, Medical University of Graz, Graz, Austria
| | - Jürgen Hartler
- Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria; Field of Excellence BioHealth, University of Graz, Graz, Austria
| | - Harald C Köfeler
- Core Facility Mass Spectrometry, Medical University of Graz, Graz, Austria
| | - Christoph Röcken
- Department of Pathology, University Hospital Schleswig Holstein, Kiel, Schleswig-Holstein, Germany
| | - Ünal Coskun
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum Munich at the University Hospital Carl Gustav Carus, Technische Universität (TU) Dresden, Dresden, Germany; German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany; Department of Membrane Biochemistry and Lipid Research, University Hospital Carl Gustav Carus of Technische Universität Dresden, Dresden, Germany
| | - Edda Klipp
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Witigo von Schoenfels
- Department of Visceral and Thoracic Surgery, University Hospital Schleswig-Holstein, Kiel Campus, Christian-Albrechts-University Kiel, Kiel, Germany; Christian Albrechts University in Kiel Center of Clinical Anatomy Kiel, Schleswig-Holstein, Germany
| | - Justus Gross
- Department of General, Visceral, Vascular and Transplant Surgery, Rostock University Medical Center, Rostock, Germany
| | - Clemens Schafmayer
- Department of General, Visceral, Vascular and Transplant Surgery, Rostock University Medical Center, Rostock, Germany
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Germany
| | - Josch Konstantin Pauling
- LipiTUM, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany.
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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6
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Hartler J, Armando AM, Trötzmüller M, Dennis EA, Köfeler HC, Quehenberger O. Automated Annotation of Sphingolipids Including Accurate Identification of Hydroxylation Sites Using MS n Data. Anal Chem 2020; 92:14054-14062. [PMID: 33003696 PMCID: PMC7581017 DOI: 10.1021/acs.analchem.0c03016] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 12/18/2022]
Abstract
Sphingolipids constitute a heterogeneous lipid category that is involved in many key cellular functions. For high-throughput analyses of sphingolipids, tandem mass spectrometry (MS/MS) is the method of choice, offering sufficient sensitivity, structural information, and quantitative precision for detecting hundreds to thousands of species simultaneously. While glycerolipids and phospholipids are predominantly non-hydroxylated, sphingolipids are typically dihydroxylated. However, species containing one or three hydroxylation sites can be detected frequently. This variability in the number of hydroxylation sites on the sphingolipid long-chain base and the fatty acyl moiety produces many more isobaric species and fragments than for other lipid categories. Due to this complexity, the automated annotation of sphingolipid species is challenging, and incorrect annotations are common. In this study, we present an extension of the Lipid Data Analyzer (LDA) "decision rule set" concept that considers the structural characteristics that are specific for this lipid category. To address the challenges inherent to automated annotation of sphingolipid structures from MS/MS data, we first developed decision rule sets using spectra from authentic standards and then tested the applicability on biological samples including murine brain and human plasma. A benchmark test based on the murine brain samples revealed a highly improved annotation quality as measured by sensitivity and reliability. The results of this benchmark test combined with the easy extensibility of the software to other (sphingo)lipid classes and the capability to detect and correctly annotate novel sphingolipid species make LDA broadly applicable to automated sphingolipid analysis, especially in high-throughput settings.
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Affiliation(s)
- Jürgen Hartler
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, 92093 California, United States.,Institute of Pharmaceutical Sciences, University of Graz, Universitätsplatz 1/I, 8010 Graz, Austria
| | - Aaron M Armando
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, 92093 California, United States
| | - Martin Trötzmüller
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstraße 24, 8010 Graz, Austria
| | - Edward A Dennis
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, 92093 California, United States
| | - Harald C Köfeler
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstraße 24, 8010 Graz, Austria
| | - Oswald Quehenberger
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, 92093 California, United States
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7
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Panzenboeck L, Troppmair N, Schlachter S, Koellensperger G, Hartler J, Rampler E. Chasing the Major Sphingolipids on Earth: Automated Annotation of Plant Glycosyl Inositol Phospho Ceramides by Glycolipidomics. Metabolites 2020; 10:metabo10090375. [PMID: 32961698 PMCID: PMC7570276 DOI: 10.3390/metabo10090375] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 08/20/2020] [Revised: 09/16/2020] [Accepted: 09/16/2020] [Indexed: 12/15/2022] Open
Abstract
Glycosyl inositol phospho ceramides (GIPCs) are the major sphingolipids on earth, as they account for a considerable fraction of the total lipids in plants and fungi, which in turn represent a large portion of the biomass on earth. Despite their obvious importance, GIPC analysis remains challenging due to the lack of commercial standards and automated annotation software. In this work, we introduce a novel GIPC glycolipidomics workflow based on reversed-phase ultra-high pressure liquid chromatography coupled to high-resolution mass spectrometry. For the first time, automated GIPC assignment was performed using the open-source software Lipid Data Analyzer (LDA), based on platform-independent decision rules. Four different plant samples (salad, spinach, raspberry, and strawberry) were analyzed and the results revealed 64 GIPCs based on accurate mass, characteristic MS2 fragments and matching retention times. Relative quantification using lactosyl ceramide for internal standardization revealed GIPC t18:1/h24:0 as the most abundant species in all plants. Depending on the plant sample, GIPCs contained mainly amine, N-acetylamine or hydroxyl residues. Most GIPCs revealed a Hex-HexA-IPC core and contained a ceramide part with a trihydroxylated t18:0 or a t18:1 long chain base and hydroxylated fatty acid chains ranging from 16 to 26 carbon atoms in length (h16:0-h26:0). Interestingly, four GIPCs containing t18:2 were observed in the raspberry sample, which was not reported so far. The presented workflow supports the characterization of different plant samples by automatic GIPC assignment, potentially leading to the identification of new GIPCs. For the first time, automated high-throughput profiling of these complex glycolipids is possible by liquid chromatography-high-resolution tandem mass spectrometry and subsequent automated glycolipid annotation based on decision rules.
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Affiliation(s)
- Lisa Panzenboeck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria; (L.P.); (N.T.); (S.S.); (G.K.)
| | - Nina Troppmair
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria; (L.P.); (N.T.); (S.S.); (G.K.)
| | - Sara Schlachter
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria; (L.P.); (N.T.); (S.S.); (G.K.)
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria; (L.P.); (N.T.); (S.S.); (G.K.)
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria
- Chemistry Meets Microbiology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Jürgen Hartler
- Institute of Pharmaceutical Sciences, University of Graz, Universitätsplatz 1/I, 8010 Graz, Austria;
| | - Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria; (L.P.); (N.T.); (S.S.); (G.K.)
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria
- Chemistry Meets Microbiology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
- Correspondence: ; Tel.: +43-1-4277-52381
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8
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Krettler CA, Hartler J, Thallinger GG. Identification and Quantification of Oxidized Lipids in LC-MS Lipidomics Data. Stud Health Technol Inform 2020; 271:39-48. [PMID: 32578539 DOI: 10.3233/shti200072] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Changes in lipid homeostasis can lead to a plethora of diseases, raising the importance of reliable identification and measurement of lipids enabled by bioinformatics tools. However, due to the enormous diversity of lipids, most contemporary tools cover only a marginal range of lipid classes. To reduce such a shortcoming, this work extends the lipid species covered by Lipid Data Analyzer (LDA) to galactolipids and oxidized lipids. Appropriate mass lists were generated for MS1 identifications and the proprietary decision rule sets were extended for MS2 identifications of the novel lipid classes. Furthermore, LDA was extended to enable identification of oxidatively modified fatty acyl chains. With these extensions, LDA can reliably identify the most important galactolipids as well as oxidatively modified versions of the 22 previously implemented lipid classes. Comparison with other up to date lipidomics tools show that LDA has a better coverage of the newly implemented lipid species. The extended version of LDA provides researchers with a powerful platform to elucidate diseases caused by perturbations in the oxidized lipidome. LDA is freely available from https://genome.tugraz.at/lda.
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Affiliation(s)
- Christoph A Krettler
- Institute of Computational Biotechnology, Graz University of Technology, Austria
| | - Jürgen Hartler
- Department of Pharmacology, University of California San Diego, USA
| | - Gerhard G Thallinger
- Institute of Computational Biotechnology, Graz University of Technology, Austria
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9
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Züllig T, Zandl-Lang M, Trötzmüller M, Hartler J, Plecko B, Köfeler HC. A Metabolomics Workflow for Analyzing Complex Biological Samples Using a Combined Method of Untargeted and Target-List Based Approaches. Metabolites 2020; 10:E342. [PMID: 32854199 PMCID: PMC7570008 DOI: 10.3390/metabo10090342] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/20/2020] [Accepted: 08/20/2020] [Indexed: 12/22/2022] Open
Abstract
In the highly dynamic field of metabolomics, we have developed a method for the analysis of hydrophilic metabolites in various biological samples. Therefore, we used hydrophilic interaction chromatography (HILIC) for separation, combined with a high-resolution mass spectrometer (MS) with the aim of separating and analyzing a wide range of compounds. We used 41 reference standards with different chemical properties to develop an optimal chromatographic separation. MS analysis was performed with a set of pooled biological samples human cerebrospinal fluid (CSF), and human plasma. The raw data was processed in a first step with Compound Discoverer 3.1 (CD), a software tool for untargeted metabolomics with the aim to create a list of unknown compounds. In a second step, we combined the results obtained with our internally analyzed reference standard list to process the data along with the Lipid Data Analyzer 2.6 (LDA), a software tool for a targeted approach. In order to demonstrate the advantages of this combined target-list based and untargeted approach, we not only compared the relative standard deviation (%RSD) of the technical replicas of pooled plasma samples (n = 5) and pooled CSF samples (n = 3) with the results from CD, but also with XCMS Online, a well-known software tool for untargeted metabolomics studies. As a result of this study we could demonstrate with our HILIC-MS method that all standards could be either separated by chromatography, including isobaric leucine and isoleucine or with MS by different mass. We also showed that this combined approach benefits from improved precision compared to well-known metabolomics software tools such as CD and XCMS online. Within the pooled plasma samples processed by LDA 68% of the detected compounds had a %RSD of less than 25%, compared to CD and XCMS online (57% and 55%). The improvements of precision in the pooled CSF samples were even more pronounced, 83% had a %RSD of less than 25% compared to CD and XCMS online (28% and 8% compounds detected). Particularly for low concentration samples, this method showed a more precise peak area integration with its 3D algorithm and with the benefits of the LDAs graphical user interface for fast and easy manual curation of peak integration. The here-described method has the advantage that manual curation for larger batch measurements remains minimal due to the target list containing the information obtained by an untargeted approach.
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Affiliation(s)
- Thomas Züllig
- Core Facility Mass Spectrometry, Medical University of Graz, 8036 Graz, Austria; (T.Z.); (M.T.)
| | - Martina Zandl-Lang
- Department of Paediatrics and Adolescent Medicine, Division of General Paediatrics, University Childrens’ Hospital Graz, Medical University of Graz, 8036 Graz, Austria; (M.Z.-L.); (B.P.)
| | - Martin Trötzmüller
- Core Facility Mass Spectrometry, Medical University of Graz, 8036 Graz, Austria; (T.Z.); (M.T.)
| | - Jürgen Hartler
- Institute of Pharmaceutical Sciences, University of Graz, 8036 Graz, Austria;
| | - Barbara Plecko
- Department of Paediatrics and Adolescent Medicine, Division of General Paediatrics, University Childrens’ Hospital Graz, Medical University of Graz, 8036 Graz, Austria; (M.Z.-L.); (B.P.)
| | - Harald C. Köfeler
- Core Facility Mass Spectrometry, Medical University of Graz, 8036 Graz, Austria; (T.Z.); (M.T.)
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10
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Hoffmann N, Hartler J, Ahrends R. jmzTab-M: A Reference Parser, Writer, and Validator for the Proteomics Standards Initiative mzTab 2.0 Metabolomics Standard. Anal Chem 2019; 91:12615-12618. [PMID: 31525911 DOI: 10.1021/acs.analchem.9b01987] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
mzTab 2.0 for metabolomics (mzTab-M) is the most recent standard format developed in collaboration by the Proteomics and Metabolomics Standards Initiatives including contributions by the recently founded Lipidomics Standards Initiative. mzTab-M is a redesign of the original mzTab format which was geared toward reporting of proteomics results and, as such, provided only limited support for metabolites. As a tab-delimited, spreadsheet-like format, mzTab-M captures experimental metadata, summary information on small molecules across assays, MS features as a basis for quantitation, and evidence to support the reporting of individual or feature group identifications. Here, we present the Java reference implementation for reading, writing, and validating mzTab-M files. Furthermore, we provide a web application for conveniently validating mzTab-M files by a graphical user interface, and a command line validator that accompanies the library. The jmzTab-M library, version 1.0.4 ( https://doi.org/10.5281/zenodo.3362151 ), is available at https://github.com/lifs-tools/jmzTab-m and from Maven Central at https://search.maven.org/search?q=jmztabm under the terms of the open source Apache License 2.0. The web application as well as the Python and R implementations are available at https://github.com/lifs-tools . The respective Web sites link to additional API documentation, as well as to usage examples.
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Affiliation(s)
- Nils Hoffmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V. , Otto-Hahn-Straße 6b , 44227 Dortmund , Germany
| | - Jürgen Hartler
- Department of Pharmacology , University of California San Diego , 9500 Gilman Drive , La Jolla , California 92093 , United States.,Institute of Computational Biotechnology , Graz University of Technology , Petersgasse 14 , 8010 Graz , Austria
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V. , Otto-Hahn-Straße 6b , 44227 Dortmund , Germany.,Department of Analytical Chemistry, Faculty of Chemistry , University of Vienna , Währinger Straße 38 , 1090 Wien , Austria
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11
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Hoffmann N, Rein J, Sachsenberg T, Hartler J, Haug K, Mayer G, Alka O, Dayalan S, Pearce JTM, Rocca-Serra P, Qi D, Eisenacher M, Perez-Riverol Y, Vizcaíno JA, Salek RM, Neumann S, Jones AR. mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics. Anal Chem 2019; 91:3302-3310. [PMID: 30688441 PMCID: PMC6660005 DOI: 10.1021/acs.analchem.8b04310] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [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: 09/21/2018] [Accepted: 01/28/2019] [Indexed: 12/29/2022]
Abstract
Mass spectrometry (MS) is one of the primary techniques used for large-scale analysis of small molecules in metabolomics studies. To date, there has been little data format standardization in this field, as different software packages export results in different formats represented in XML or plain text, making data sharing, database deposition, and reanalysis highly challenging. Working within the consortia of the Metabolomics Standards Initiative, Proteomics Standards Initiative, and the Metabolomics Society, we have created mzTab-M to act as a common output format from analytical approaches using MS on small molecules. The format has been developed over several years, with input from a wide range of stakeholders. mzTab-M is a simple tab-separated text format, but importantly, the structure is highly standardized through the design of a detailed specification document, tightly coupled to validation software, and a mandatory controlled vocabulary of terms to populate it. The format is able to represent final quantification values from analyses, as well as the evidence trail in terms of features measured directly from MS (e.g., LC-MS, GC-MS, DIMS, etc.) and different types of approaches used to identify molecules. mzTab-M allows for ambiguity in the identification of molecules to be communicated clearly to readers of the files (both people and software). There are several implementations of the format available, and we anticipate widespread adoption in the field.
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Affiliation(s)
- Nils Hoffmann
- Leibniz-Institut
für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Straße 6b, 44227 Dortmund, Germany
| | - Joel Rein
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Timo Sachsenberg
- Applied Bioinformatics
Group, Center for Bioinformatics, University
of Tübingen, Sand
14, 72076 Tübingen, Germany
| | - Jürgen Hartler
- Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
- Center
for Explorative Lipidomics, BioTechMed-Graz, 8010 Graz, Austria
| | - Kenneth Haug
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Gerhard Mayer
- Medizinisches Proteom Center (MPC), Ruhr-Universität
Bochum, Universitätsstraße
150, D-44801 Bochum, Germany
| | - Oliver Alka
- Applied Bioinformatics
Group, Center for Bioinformatics, University
of Tübingen, Sand
14, 72076 Tübingen, Germany
| | - Saravanan Dayalan
- Metabolomics Australia, The University
of Melbourne, Parkville, Victoria 3010, Australia
| | - Jake T. M. Pearce
- MRC-NIHR National Phenome Centre, Department of Surgery & Cancer, Imperial College London, London SW7 2AZ, United Kingdom
| | - Philippe Rocca-Serra
- University of Oxford, e-Research Centre, 7 Keble Road, Oxford OX1
3QG, United Kingdom
| | - Da Qi
- BGI-Shenzhen, Shenzhen, 518083, People’s Republic of China
- Institute
of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Martin Eisenacher
- Medizinisches Proteom Center (MPC), Ruhr-Universität
Bochum, Universitätsstraße
150, D-44801 Bochum, Germany
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Reza M. Salek
- International Agency for Research on Cancer, 150 cours Albert Thomas, 69008 Lyon, France
| | - Steffen Neumann
- Department
of Stress and Developmental Biology, Leibniz
Institute of Plant Biochemistry, 06120 Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig Deutscher, Platz
5e, 04103 Leipzig, Germany
| | - Andrew R. Jones
- Institute
of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
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12
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Hartler J, Triebl A, Ziegl A, Trötzmüller M, Rechberger GN, Zeleznik OA, Zierler KA, Torta F, Cazenave-Gassiot A, Wenk MR, Fauland A, Wheelock CE, Armando AM, Quehenberger O, Zhang Q, Wakelam MJO, Haemmerle G, Spener F, Köfeler HC, Thallinger GG. Deciphering lipid structures based on platform-independent decision rules. Nat Methods 2017; 14:1171-1174. [PMID: 29058722 PMCID: PMC5988032 DOI: 10.1038/nmeth.4470] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [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: 05/20/2017] [Accepted: 09/19/2017] [Indexed: 11/23/2022]
Abstract
We achieve automated and reliable annotation of lipid species and their molecular structures in high-throughput data from chromatography-coupled tandem mass spectrometry using decision rule sets embedded in Lipid Data Analyzer (LDA; http://genome.tugraz.at/lda2). Using various low- and high-resolution mass spectrometry instruments with several collision energies, we proved the method's platform independence. We propose that the software's reliability, flexibility, and ability to identify novel lipid molecular species may now render current state-of-the-art lipid libraries obsolete.
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Affiliation(s)
- Jürgen Hartler
- Institute of Computational Biotechnology, Graz University of Technology, Graz, Austria
- Center for Medical Research, Medical University of Graz, Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Graz, Austria
| | - Alexander Triebl
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - Andreas Ziegl
- Institute of Computational Biotechnology, Graz University of Technology, Graz, Austria
| | - Martin Trötzmüller
- Center for Medical Research, Medical University of Graz, Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Graz, Austria
| | - Gerald N Rechberger
- Omics Center Graz, BioTechMed-Graz, Graz, Austria
- Department of Molecular Biosciences, University of Graz, Graz, Austria
| | - Oana A Zeleznik
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, U.S.A
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, U.S.A
| | - Kathrin A Zierler
- Department of Molecular Biosciences, University of Graz, Graz, Austria
| | - Federico Torta
- Singapore Lipidomics Incubator, National University of Singapore, Singapore, Singapore
| | | | - Markus R Wenk
- Singapore Lipidomics Incubator, National University of Singapore, Singapore, Singapore
| | - Alexander Fauland
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Craig E Wheelock
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Aaron M Armando
- School of Medicine, University of California San Diego, La Jolla, California, U.S.A
| | - Oswald Quehenberger
- School of Medicine, University of California San Diego, La Jolla, California, U.S.A
| | - Qifeng Zhang
- The Babraham Institute, Babraham Research Campus, Cambridge, U.K
| | | | - Guenter Haemmerle
- Department of Molecular Biosciences, University of Graz, Graz, Austria
| | - Friedrich Spener
- Department of Molecular Biosciences, University of Graz, Graz, Austria
- Department of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Harald C Köfeler
- Center for Medical Research, Medical University of Graz, Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Graz, Austria
| | - Gerhard G Thallinger
- Institute of Computational Biotechnology, Graz University of Technology, Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Graz, Austria
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13
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Pauling JK, Hermansson M, Hartler J, Christiansen K, Gallego SF, Peng B, Ahrends R, Ejsing CS. Proposal for a common nomenclature for fragment ions in mass spectra of lipids. PLoS One 2017; 12:e0188394. [PMID: 29161304 PMCID: PMC5697860 DOI: 10.1371/journal.pone.0188394] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [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: 07/03/2017] [Accepted: 10/20/2017] [Indexed: 12/16/2022] Open
Abstract
Advances in mass spectrometry-based lipidomics have in recent years prompted efforts to standardize the annotation of the vast number of lipid molecules that can be detected in biological systems. These efforts have focused on cataloguing, naming and drawing chemical structures of intact lipid molecules, but have provided no guidelines for annotation of lipid fragment ions detected using tandem and multi-stage mass spectrometry, albeit these fragment ions are mandatory for structural elucidation and high confidence lipid identification, especially in high throughput lipidomics workflows. Here we propose a nomenclature for the annotation of lipid fragment ions, describe its implementation and present a freely available web application, termed ALEX123 lipid calculator, that can be used to query a comprehensive database featuring curated lipid fragmentation information for more than 430,000 potential lipid molecules from 47 lipid classes covering five lipid categories. We note that the nomenclature is generic, extendable to stable isotope-labeled lipid molecules and applicable to automated annotation of fragment ions detected by most contemporary lipidomics platforms, including LC-MS/MS-based routines.
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Affiliation(s)
- Josch K. Pauling
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Martin Hermansson
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Jürgen Hartler
- Institute of Computational Biotechnology, Graz University of Technology, Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Graz, Austria
| | - Klaus Christiansen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Sandra F. Gallego
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Bing Peng
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
| | - Christer S. Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- * E-mail:
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14
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Trötzmüller M, Triebl A, Ajsic A, Hartler J, Köfeler H, Regittnig W. Determination of the Isotopic Enrichment of 13C- and 2H-Labeled Tracers of Glucose Using High-Resolution Mass Spectrometry: Application to Dual- and Triple-Tracer Studies. Anal Chem 2017; 89:12252-12260. [DOI: 10.1021/acs.analchem.7b03134] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Martin Trötzmüller
- Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse
24, 8010 Graz, Austria
| | | | | | - Jürgen Hartler
- Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse
24, 8010 Graz, Austria
- Institute of Computational
Biotechnology, Graz University of Technology, Petersgasse 14, A-8010 Graz, Austria
| | - Harald Köfeler
- Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse
24, 8010 Graz, Austria
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15
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Triebl A, Trötzmüller M, Hartler J, Stojakovic T, Köfeler HC. Lipidomics by ultrahigh performance liquid chromatography-high resolution mass spectrometry and its application to complex biological samples. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1053:72-80. [PMID: 28415015 DOI: 10.1016/j.jchromb.2017.03.027] [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: 11/29/2016] [Revised: 03/08/2017] [Accepted: 03/22/2017] [Indexed: 01/21/2023]
Abstract
An improved approach for selective and sensitive identification and quantitation of lipid molecular species using reversed phase chromatography coupled to high resolution mass spectrometry was developed. The method is applicable to a wide variety of biological matrices using a simple liquid-liquid extraction procedure. Together, this approach combines multiple selectivity criteria: Reversed phase chromatography separates lipids according to their acyl chain length and degree of unsaturation and is capable of resolving positional isomers of lysophospholipids, as well as structural isomers of diacyl phospholipids and glycerolipids. Orbitrap mass spectrometry delivers the elemental composition of both positive and negative ions with high mass accuracy. Finally, automatically generated tandem mass spectra provide structural insight into numerous glycerolipids, phospholipids, and sphingolipids within a single run. Calibration showed linearity ranges of more than four orders of magnitude, good values for accuracy and precision at biologically relevant concentration levels, and limits of quantitation of a few femtomoles on column. Hundreds of lipid molecular species were detected and quantified in three different biological matrices, which cover well the wide variety and complexity of various model organisms in lipidomic research. Together with a software package, this method is a prime choice for global lipidomic analysis of even the most complex biological samples.
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Affiliation(s)
- Alexander Triebl
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Martin Trötzmüller
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria.
| | - Jürgen Hartler
- Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
| | - Tatjana Stojakovic
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria
| | - Harald C Köfeler
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria; Omics Center Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
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16
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Triebl A, Hartler J, Trötzmüller M, C Köfeler H. Lipidomics: Prospects from a technological perspective. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1862:740-746. [PMID: 28341148 DOI: 10.1016/j.bbalip.2017.03.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [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: 11/30/2016] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 12/16/2022]
Abstract
Over the last two decades, lipidomics has evolved into an 'omics' technology pari passu with benchmarking 'omics' technologies, such as genomics or proteomics. The driving force behind this development was a constant advance in mass spectrometry and related technologies. The aim of this opinion article is to give the interested reader a concise but still comprehensive overview about the technological state of the art in lipidomics, current challenges and perspectives for future development. As such, this article guides through the whole workflow of lipidomics, from sampling to data analysis. This article is part of a Special Issue entitled: BBALIP_Lipidomics Opinion Articles edited by Sepp Kohlwein.
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Affiliation(s)
- Alexander Triebl
- Center for Medical Research (ZMF), Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Jürgen Hartler
- Center for Medical Research (ZMF), Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria; Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria; Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Martin Trötzmüller
- Center for Medical Research (ZMF), Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Harald C Köfeler
- Center for Medical Research (ZMF), Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria; Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010 Graz, Austria.
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17
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Eichmann TO, Grumet L, Taschler U, Hartler J, Heier C, Woblistin A, Pajed L, Kollroser M, Rechberger G, Thallinger GG, Zechner R, Haemmerle G, Zimmermann R, Lass A. ATGL and CGI-58 are lipid droplet proteins of the hepatic stellate cell line HSC-T6. J Lipid Res 2015; 56:1972-84. [PMID: 26330055 PMCID: PMC4583087 DOI: 10.1194/jlr.m062372] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Indexed: 12/31/2022] Open
Abstract
Lipid droplets (LDs) of hepatic stellate cells (HSCs) contain large amounts of vitamin A [in the form of retinyl esters (REs)] as well as other neutral lipids such as TGs. During times of insufficient vitamin A availability, RE stores are mobilized to ensure a constant supply to the body. To date, little is known about the enzymes responsible for the hydrolysis of neutral lipid esters, in particular of REs, in HSCs. In this study, we aimed to identify LD-associated neutral lipid hydrolases by a proteomic approach using the rat stellate cell line HSC-T6. First, we loaded cells with retinol and FAs to promote lipid synthesis and deposition within LDs. Then, LDs were isolated and lipid composition and the LD proteome were analyzed. Among other proteins, we found perilipin 2, adipose TG lipase (ATGL), and comparative gene identification-58 (CGI-58), known and established LD proteins. Bioinformatic search of the LD proteome for α/β-hydrolase fold-containing proteins revealed no yet uncharacterized neutral lipid hydrolases. In in vitro activity assays, we show that rat (r)ATGL, coactivated by rat (r)CGI-58, efficiently hydrolyzes TGs and REs. These findings suggest that rATGL and rCGI-58 are LD-resident proteins in HSCs and participate in the mobilization of both REs and TGs.
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Affiliation(s)
- Thomas O Eichmann
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Lukas Grumet
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Ulrike Taschler
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Jürgen Hartler
- Bioinformatics, Institute for Knowledge Discovery, Graz University of Technology, Graz, Austria
| | - Christoph Heier
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Aaron Woblistin
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Laura Pajed
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Manfred Kollroser
- Institute of Forensic Medicine, Medical University of Graz, Graz, Austria
| | - Gerald Rechberger
- Institute of Molecular Biosciences, University of Graz, Graz, Austria BioTechMed-Graz, Graz, Austria OMICS Center, Graz, Austria
| | - Gerhard G Thallinger
- Bioinformatics, Institute for Knowledge Discovery, Graz University of Technology, Graz, Austria BioTechMed-Graz, Graz, Austria OMICS Center, Graz, Austria
| | - Rudolf Zechner
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Günter Haemmerle
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Robert Zimmermann
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Achim Lass
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
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18
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Sala P, Pötz S, Brunner M, Trötzmüller M, Fauland A, Triebl A, Hartler J, Lankmayr E, Köfeler HC. Determination of oxidized phosphatidylcholines by hydrophilic interaction liquid chromatography coupled to Fourier transform mass spectrometry. Int J Mol Sci 2015; 16:8351-63. [PMID: 25874761 PMCID: PMC4425085 DOI: 10.3390/ijms16048351] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 04/02/2015] [Accepted: 04/08/2015] [Indexed: 01/08/2023] Open
Abstract
A novel liquid chromatography-mass spectrometry (LC-MS) approach for analysis of oxidized phosphatidylcholines by an Orbitrap Fourier Transform mass spectrometer in positive electrospray ionization (ESI) coupled to hydrophilic interaction liquid chromatography (HILIC) was developed. This method depends on three selectivity criteria for separation and identification: retention time, exact mass at a resolution of 100,000 and collision induced dissociation (CID) fragment spectra in a linear ion trap. The process of chromatography development showed the best separation properties with a silica-based Kinetex column. This type of chromatography was able to separate all major lipid classes expected in mammalian samples, yielding increased sensitivity of oxidized phosphatidylcholines over reversed phase chromatography. Identification of molecular species was achieved by exact mass on intact molecular ions and CID tandem mass spectra containing characteristic fragments. Due to a lack of commercially available standards, method development was performed with copper induced oxidation products of palmitoyl-arachidonoyl-phosphatidylcholine, which resulted in a plethora of lipid species oxidized at the arachidonoyl moiety. Validation of the method was done with copper oxidized human low-density lipoprotein (LDL) prepared by ultracentrifugation. In these LDL samples we could identify 46 oxidized molecular phosphatidylcholine species out of 99 possible candidates.
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Affiliation(s)
- Pia Sala
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
- Institute of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse 9/II, Graz 8010, Austria.
| | - Sandra Pötz
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
- Institute of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse 9/II, Graz 8010, Austria.
| | - Martina Brunner
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
| | - Martin Trötzmüller
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
| | - Alexander Fauland
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
- Institute of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse 9/II, Graz 8010, Austria.
| | - Alexander Triebl
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
| | - Jürgen Hartler
- Bioinformatics Group, Institute for Knowledge Discovery, Graz University of Technology, Petersgasse 14, Graz 8010, Austria.
- Omics Center Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
| | - Ernst Lankmayr
- Institute of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse 9/II, Graz 8010, Austria.
| | - Harald C Köfeler
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
- Omics Center Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
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19
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Nasso S, Hartler J, Trajanoski Z, Di Camillo B, Mechtler K, Toffolo GM. 3DSpectra: A 3-dimensional quantification algorithm for LC-MS labeled profile data. J Proteomics 2015; 112:156-65. [PMID: 25218586 DOI: 10.1016/j.jprot.2014.08.017] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 07/25/2014] [Accepted: 08/12/2014] [Indexed: 10/24/2022]
Abstract
UNLABELLED Mass spectrometry-based proteomics can generate highly informative datasets, as profile three-dimensional (3D) LC-MS data: LC-MS separates peptides in two dimensions (time, m/z) minimizing their overlap, and profile acquisition enhances quantification. To exploit both data features, we developed 3DSpectra, a 3D approach embedding a statistical method for peptide border recognition. 3DSpectra efficiently accesses profile data by means of mzRTree, and makes use of a priori metadata, provided by search engines, to quantify the identified peptides. An isotopic distribution model, shaped by a bivariate Gaussian Mixture Model (GMM), which includes a noise component, is fitted to the peptide peaks using the expectation-maximization (EM) approach. The EM starting parameters, i.e., the centers and shapes of the Gaussians, are retrieved from the metadata. The borders of the peaks are delimited by the GMM iso-density curves, and noisy or outlying data are discarded from subsequent analysis. The 3DSpectra program was compared to ASAPRatio for a controlled mixture of Isotope-Coded Protein Labels (ICPL) labeled proteins, which were mixed at predefined ratios and acquired in enhanced profile mode, in triplicate. The 3DSpectra software showed significantly higher linearity, quantification accuracy, and precision than did ASAPRatio in this real use case simulation where the true ratios are known, and it also achieved wider peptide coverage and dynamic range. BIOLOGICAL SIGNIFICANCE Quantitative proteomics is pivotal for many systems biology related fields, such as biomarker discovery. The quantification quality provided by the adopted software is crucial for the success of protein differential expression studies. To determine the reliability of a quantitative computational method, we suggest evaluating performance parameters like accuracy and precision of the quantifications, robustness to outliers and proteome coverage. A quantitative comparison of these parameters is highly desirable since it enables to benchmark software performance. We applied this strategy to 3DSpectra, a 3-dimensional approach to spectra analysis for MS1 peptide quantification. It distinguishes peptide peaks from spurious peaks interfering in the survey scan. 3DSpectra was compared to ASAPRatio in terms of quantification quality performance parameters and showed an overall improvement.
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Affiliation(s)
- S Nasso
- Department of Biology, Institute of Molecular Systems Biology, ETH, Auguste-Piccard-Hof 1, ETH Honggerberg, CH-8093 Zürich, Switzerland; Department of Information Engineering, University of Padova, Via Gradenigo, 6/B, 35131 Padova, Italy.
| | - J Hartler
- Bioinformatics Group, Institute for Knowledge Discovery, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
| | - Z Trajanoski
- Biocenter, Division for Bioinformatics, Innsbruck Medical University, Innrain 80, 6010 Innsbruck, Austria
| | - B Di Camillo
- Department of Information Engineering, University of Padova, Via Gradenigo, 6/B, 35131 Padova, Italy
| | - K Mechtler
- Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, A-1030 Vienna, Austria
| | - G M Toffolo
- Department of Information Engineering, University of Padova, Via Gradenigo, 6/B, 35131 Padova, Italy
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20
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Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG, Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu QW, Del Toro N, Pérez-Riverol Y, Ghali F, Bandeira N, Xenarios I, Kohlbacher O, Vizcaíno JA, Hermjakob H. The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience. Mol Cell Proteomics 2014; 13:2765-75. [PMID: 24980485 PMCID: PMC4189001 DOI: 10.1074/mcp.o113.036681] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [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: 11/06/2022] Open
Abstract
The HUPO Proteomics Standards Initiative has developed several standardized data formats to facilitate data sharing in mass spectrometry (MS)-based proteomics. These allow researchers to report their complete results in a unified way. However, at present, there is no format to describe the final qualitative and quantitative results for proteomics and metabolomics experiments in a simple tabular format. Many downstream analysis use cases are only concerned with the final results of an experiment and require an easily accessible format, compatible with tools such as Microsoft Excel or R. We developed the mzTab file format for MS-based proteomics and metabolomics results to meet this need. mzTab is intended as a lightweight supplement to the existing standard XML-based file formats (mzML, mzIdentML, mzQuantML), providing a comprehensive summary, similar in concept to the supplemental material of a scientific publication. mzTab files can contain protein, peptide, and small molecule identifications together with experimental metadata and basic quantitative information. The format is not intended to store the complete experimental evidence but provides mechanisms to report results at different levels of detail. These range from a simple summary of the final results to a representation of the results including the experimental design. This format is ideally suited to make MS-based proteomics and metabolomics results available to a wider biological community outside the field of MS. Several software tools for proteomics and metabolomics have already adapted the format as an output format. The comprehensive mzTab specification document and extensive additional documentation can be found online.
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Affiliation(s)
- Johannes Griss
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK; §Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Andrew R Jones
- ‖Institute of Integrative Biology, University of Liverpool, L69 7ZB, Liverpool, UK
| | - Timo Sachsenberg
- **Center for Bioinformatics and Department of Computer Science, University of Tübingen, D-72076 Tübingen, Germany
| | - Mathias Walzer
- **Center for Bioinformatics and Department of Computer Science, University of Tübingen, D-72076 Tübingen, Germany
| | - Laurent Gatto
- ‡‡Computational Proteomics Unit and Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, CB2 1QR, Cambridge, UK
| | - Jürgen Hartler
- §§Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14/V, 8010 Graz, Austria; ¶¶Core Facility Bioinformatics, Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14/V, 8010 Graz, Austria
| | - Gerhard G Thallinger
- §§Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14/V, 8010 Graz, Austria; ¶¶Core Facility Bioinformatics, Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14/V, 8010 Graz, Austria
| | - Reza M Salek
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK
| | - Christoph Steinbeck
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK
| | - Nadin Neuhauser
- ‖‖Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Jürgen Cox
- ‖‖Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Steffen Neumann
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany
| | - Jun Fan
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Florian Reisinger
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK
| | - Qing-Wei Xu
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK; College of Computer, Hubei University of Education, Wuhan, China
| | - Noemi Del Toro
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK
| | - Yasset Pérez-Riverol
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK
| | - Fawaz Ghali
- ‖Institute of Integrative Biology, University of Liverpool, L69 7ZB, Liverpool, UK
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, CA
| | - Ioannis Xenarios
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, 1 Rue Michel Servet, 1211 Geneva, Switzerland; Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, Genopode 1015 Lausanne; Center of Integrative Genomics, University of Lausanne, Quartier Sorge Genopode, 1015 Lausanne
| | - Oliver Kohlbacher
- **Center for Bioinformatics and Department of Computer Science, University of Tübingen, D-72076 Tübingen, Germany; Quantitative Biology Center, University of Tübingen, D-72076 Tübingen, Germany
| | - Juan Antonio Vizcaíno
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK;
| | - Henning Hermjakob
- From the ‡European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK
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21
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Triebl A, Trötzmüller M, Eberl A, Hanel P, Hartler J, Köfeler HC. Quantitation of phosphatidic acid and lysophosphatidic acid molecular species using hydrophilic interaction liquid chromatography coupled to electrospray ionization high resolution mass spectrometry. J Chromatogr A 2014; 1347:104-10. [PMID: 24813932 DOI: 10.1016/j.chroma.2014.04.070] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [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: 01/27/2014] [Revised: 03/27/2014] [Accepted: 04/22/2014] [Indexed: 10/25/2022]
Abstract
A method for a highly selective and sensitive identification and quantitation of lysophosphatidic acid (LPA) and phosphatidic acid (PA) molecular species was developed using hydrophilic interaction liquid chromatography (HILIC) followed by negative-ion electrospray ionization high resolution mass spectrometry. Different extraction methods for the polar LPA and PA species were compared and a modified Bligh & Dyer extraction by addition of 0.1M hydrochloric acid resulted in a ≈1.2-fold increase of recovery for the 7 PA and a more than 15-fold increase for the 6 LPA molecular species of a commercially available natural mix compared to conventional Bligh & Dyer extraction. This modified Bligh & Dyer extraction did not show any artifacts resulting from hydrolysis of natural abundant phospholipids. The developed HILIC method is able to separate all PA and LPA species from major polar membrane lipid classes which might have suppressive effects on the minor abundant lipid classes of interest. The elemental compositions of intact lipid species are provided by the high mass resolution of 100,000 and high mass accuracy below 3ppm of the Orbitrap instrument. Additionally, tandem mass spectra were generated in a parallel data dependent acquisition mode in the linear ion trap to provide structural information at molecular level. Limits of quantitation were identified at 45fmol on column and the dynamic range reaches 20pmol on column, covering the range of natural abundance well. By applying the developed method to mouse brain it can be shown that phosphatidic acid contains less unsaturated fatty acids with PA 34:1 and PA 36:1 as the major species. In contrast, for LPA species a high content of polyunsaturated fatty acids (LPA 20:4 and LPA 22:6) was quantified.
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Affiliation(s)
- Alexander Triebl
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Martin Trötzmüller
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria; Omics Center Graz, Stiftingtalstrasse 24, 8010 Graz, Austria.
| | - Anita Eberl
- HEALTH - Institute for Biomedicine and Health Sciences, Joanneum Research Forschungsgesellschaft m.b.H., Graz, Austria
| | - Pia Hanel
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Jürgen Hartler
- Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria; Omics Center Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Harald C Köfeler
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria; Omics Center Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
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22
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Chitraju C, Trötzmüller M, Hartler J, Wolinski H, Thallinger GG, Haemmerle G, Zechner R, Zimmermann R, Köfeler HC, Spener F. The impact of genetic stress by ATGL deficiency on the lipidome of lipid droplets from murine hepatocytes. J Lipid Res 2013; 54:2185-2194. [PMID: 23740967 DOI: 10.1194/jlr.m037952] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [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: 12/21/2022] Open
Abstract
We showed earlier that nutritional stress like starvation or high-fat diet resulted in phenotypic changes in the lipidomes of hepatocyte lipid droplets (LDs), representative for the pathophysiological status of the mouse model. Here we extend our former study by adding genetic stress due to knockout (KO) of adipocyte triglyceride lipase (ATGL), the rate limiting enzyme in LD lipolysis. An intervention trial for 6 weeks with male wild-type (WT) and ATGL-KO mice was carried out; both genotypes were fed lab chow or were exposed to short-time starvation. Isolated LDs were analyzed by LC-MS/MS. Triacylglycerol, diacylglycerol, and phosphatidylcholine lipidomes, in that order, provided the best phenotypic signatures characteristic for respective stresses applied to the animals. This was evidenced at lipid species level by principal component analysis, calculation of average values for chain-lengths and numbers of double bonds, and by visualization in heat maps. Structural backgrounds for analyses and metabolic relationships were elaborated at lipid molecular species level. Relating our lipidomic data to nonalcoholic fatty liver diseases of nutritional and genetic etiologies with or without accompanying insulin resistance, phenotypic distinction in hepatocyte LDs dependent on insulin status emerged. Taken together, lipidomes of hepatocyte LDs are sensitive responders to nutritional and genetic stress.
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Affiliation(s)
- Chandramohan Chitraju
- Department of Molecular Biosciences, University of Graz, Lipidomics Research Center, 8010 Graz, Austria
| | - Martin Trötzmüller
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Lipidomics Research Center, 8010 Graz, Austria; and
| | - Jürgen Hartler
- Institute for Genomics and Bioinformatics, Graz University of Technology, and Core Facility Bioinformatics, Austrian Centre for Industrial Biotechnology, 8010 Graz, Austria
| | - Heimo Wolinski
- Department of Molecular Biosciences, University of Graz, Lipidomics Research Center, 8010 Graz, Austria
| | - Gerhard G Thallinger
- Institute for Genomics and Bioinformatics, Graz University of Technology, and Core Facility Bioinformatics, Austrian Centre for Industrial Biotechnology, 8010 Graz, Austria
| | - Guenter Haemmerle
- Department of Molecular Biosciences, University of Graz, Lipidomics Research Center, 8010 Graz, Austria
| | - Rudolf Zechner
- Department of Molecular Biosciences, University of Graz, Lipidomics Research Center, 8010 Graz, Austria
| | - Robert Zimmermann
- Department of Molecular Biosciences, University of Graz, Lipidomics Research Center, 8010 Graz, Austria
| | - Harald C Köfeler
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Lipidomics Research Center, 8010 Graz, Austria; and
| | - Friedrich Spener
- Department of Molecular Biosciences, University of Graz, Lipidomics Research Center, 8010 Graz, Austria.
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23
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Ubaida Mohien C, Colquhoun DR, Mathias DK, Gibbons JG, Armistead JS, Rodriguez MC, Rodriguez MH, Edwards NJ, Hartler J, Thallinger GG, Graham DR, Martinez-Barnetche J, Rokas A, Dinglasan RR. A bioinformatics approach for integrated transcriptomic and proteomic comparative analyses of model and non-sequenced anopheline vectors of human malaria parasites. Mol Cell Proteomics 2012; 12:120-31. [PMID: 23082028 PMCID: PMC3536893 DOI: 10.1074/mcp.m112.019596] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [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: 12/19/2022] Open
Abstract
Malaria morbidity and mortality caused by both Plasmodium falciparum and Plasmodium vivax extend well beyond the African continent, and although P. vivax causes between 80 and 300 million severe cases each year, vivax transmission remains poorly understood. Plasmodium parasites are transmitted by Anopheles mosquitoes, and the critical site of interaction between parasite and host is at the mosquito's luminal midgut brush border. Although the genome of the “model” African P. falciparum vector, Anopheles gambiae, has been sequenced, evolutionary divergence limits its utility as a reference across anophelines, especially non-sequenced P. vivax vectors such as Anopheles albimanus. Clearly, technologies and platforms that bridge this substantial scientific gap are required in order to provide public health scientists with key transcriptomic and proteomic information that could spur the development of novel interventions to combat this disease. To our knowledge, no approaches have been published that address this issue. To bolster our understanding of P. vivax–An. albimanus midgut interactions, we developed an integrated bioinformatic-hybrid RNA-Seq-LC-MS/MS approach involving An. albimanus transcriptome (15,764 contigs) and luminal midgut subproteome (9,445 proteins) assembly, which, when used with our custom Diptera protein database (685,078 sequences), facilitated a comparative proteomic analysis of the midgut brush borders of two important malaria vectors, An. gambiae and An. albimanus.
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Affiliation(s)
- Ceereena Ubaida Mohien
- W Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health & Malaria Research Institute, Baltimore, Maryland 21205, USA
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24
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Chitraju C, Trötzmüller M, Hartler J, Wolinski H, Thallinger GG, Lass A, Zechner R, Zimmermann R, Köfeler HC, Spener F. Lipidomic analysis of lipid droplets from murine hepatocytes reveals distinct signatures for nutritional stress. J Lipid Res 2012; 53:2141-2152. [PMID: 22872753 DOI: 10.1194/jlr.m028902] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Liver steatosis can be induced by fasting or high-fat diet. We investigated by lipidomic analysis whether such metabolic states are reflected in the lipidome of hepatocyte lipid droplets (LDs) from mice fed normal chow diet (FED), fasted (FAS), or fed a high-fat diet (HFD). LC-MS/MS at levels of lipid species profiles and of lipid molecular species uncovered a FAS phenotype of LD enriched in triacylglycerol (TG) molecular species with very long-chain (VLC)-PUFA residues and an HFD phenotype with less unsaturated TG species in addition to characteristic lipid marker species. Nutritional stress did not result in dramatic structural alterations in diacylglycerol (DG) and phospholipid (PL) classes. Moreover, molecular species of bulk TG and of DG indicated concomitant de novo TG synthesis and lipase-catalyzed degradation to be active in LDs. DG species with VLC-PUFA residues would be preferred precursors for phosphatidylcholine (PC) species, the others for TG molecular species. In addition, molecular species of PL classes fitted the hepatocyte Kennedy and phosphatidylethanolamine methyltransferase pathways. We demonstrate that lipidomic analysis of LDs enables phenotyping of nutritional stress. TG species are best suited for such phenotyping, whereas structural analysis of TG, DG, and PL molecular species provides metabolic insights.
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Affiliation(s)
- Chandramohan Chitraju
- Department of Molecular Biosciences, University of Graz, Lipidomics Research Center, 8010 Graz, Austria
| | - Martin Trötzmüller
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Lipidomics Research Center, 8010 Graz, Austria
| | - Jürgen Hartler
- Institute for Genomics and Bioinformatics, Graz University of Technology, and Core Facility Bioinformatics, Austrian Centre for Industrial Biotechnology, 8010 Graz, Austria
| | - Heimo Wolinski
- Department of Molecular Biosciences, University of Graz, Lipidomics Research Center, 8010 Graz, Austria
| | - Gerhard G Thallinger
- Institute for Genomics and Bioinformatics, Graz University of Technology, and Core Facility Bioinformatics, Austrian Centre for Industrial Biotechnology, 8010 Graz, Austria
| | - Achim Lass
- Department of Molecular Biosciences, University of Graz, Lipidomics Research Center, 8010 Graz, Austria
| | - Rudolf Zechner
- Department of Molecular Biosciences, University of Graz, Lipidomics Research Center, 8010 Graz, Austria
| | - Robert Zimmermann
- Department of Molecular Biosciences, University of Graz, Lipidomics Research Center, 8010 Graz, Austria
| | - Harald C Köfeler
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Lipidomics Research Center, 8010 Graz, Austria
| | - Friedrich Spener
- Department of Molecular Biosciences, University of Graz, Lipidomics Research Center, 8010 Graz, Austria.
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Hartler J, Tharakan R, Köfeler HC, Graham DR, Thallinger GG. Bioinformatics tools and challenges in structural analysis of lipidomics MS/MS data. Brief Bioinform 2012; 14:375-90. [PMID: 22764120 DOI: 10.1093/bib/bbs030] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [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: 02/01/2023] Open
Abstract
Lipidomics, the systematic study of the lipid composition of a cell or tissue, is an invaluable complement to knowledge gained by genomics and proteomics research. Mass spectrometry provides a means to detect hundreds of lipids in parallel, and this includes low abundance species of lipids. Nevertheless, frequently occurring isobaric and isomeric lipid species complicate lipidomics analyses from an analytical and bioinformatics perspective. Various MS/MS strategies have evolved to resolve ambiguous identifications of lipid species, and these strategies have been supported by corresponding bioinformatics analysis tools. This review intends to familiarize readers with available bioinformatics MS/MS analysis tools and databases, the structural information obtainable from these, and their applicability to different MS/MS strategies. Finally, future challenges in detecting double bond positions are investigated from a bioinformatics perspective.
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Fauland A, Köfeler H, Trötzmüller M, Knopf A, Hartler J, Eberl A, Chitraju C, Lankmayr E, Spener F. A comprehensive method for lipid profiling by liquid chromatography-ion cyclotron resonance mass spectrometry. J Lipid Res 2011; 52:2314-2322. [PMID: 21960706 DOI: 10.1194/jlr.d016550] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
This work aims to combine chromatographic retention, high mass resolution and accuracy, MS/MS spectra, and a package for automated identification and quantitation of lipid species in one platform for lipidomic analysis. The instrumental setup elaborated comprises reversed-phase HPLC coupled to a Fourier transform ion cyclotron resonance mass spectrometer (LTQ-FT), and Lipid Data Analyzer (LDA) software. Data analysis for lipid species quantification in this platform is based on retention time, mass resolution of 200,000, and mass accuracy below 2 ppm. In addition, automatically generated MS/MS spectra provide structural information at molecular level. This LC/MS technology allows analyzing complex biological samples in a quantitative manner as shown here paradigmatically for murine lipid droplets having a huge surplus of triacylglycerol species. Chromatographic preseparation of the bulk lipid class alleviates the problem of ion suppression of lipid species from other classes. Extension of 1D to 2D chromatography is possible, yet time consuming. The platform affords unambiguous detection of lipid species as low as 0.1‰ within major lipid classes. Taken together, a novel lipidomic LC/MS platform based on chromatographic retention, high mass resolution and accuracy, MS/MS analysis, and quantitation software enables analysis of complex samples as demonstrated for lipid droplets.
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Affiliation(s)
- Alexander Fauland
- Institute of Analytical Chemistry and Food Chemistry Graz University of Technology, Graz, Austria
| | - Harald Köfeler
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Graz, Austria.
| | - Martin Trötzmüller
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Graz, Austria
| | - Astrid Knopf
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Graz, Austria
| | - Jürgen Hartler
- Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria
| | - Anita Eberl
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Graz, Austria
| | | | - Ernst Lankmayr
- Institute of Analytical Chemistry and Food Chemistry Graz University of Technology, Graz, Austria
| | - Friedrich Spener
- Department of Molecular Biology and Biochemistry Medical University of Graz, Graz, Austria; Department of Molecular Biosciences University of Graz, Graz, Austria
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Hartler J, Trötzmüller M, Chitraju C, Spener F, Köfeler HC, Thallinger GG. Lipid Data Analyzer: unattended identification and quantitation of lipids in LC-MS data. ACTA ACUST UNITED AC 2010; 27:572-7. [PMID: 21169379 DOI: 10.1093/bioinformatics/btq699] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION The accurate measurement of the lipidome permits insights into physiological and pathological processes. Of the present high-throughput technologies, LC-MS especially bears potential of monitoring quantitative changes in hundreds of lipids simultaneously. In order to extract valuable information from huge amount of mass spectrometry data, the aid of automated, reliable, highly sensitive and specific analysis algorithms is indispensable. RESULTS We present here a novel approach for the quantitation of lipids in LC-MS data. The new algorithm obtains its analytical power by two major innovations: (i) a 3D algorithm that confines the peak borders in m/z and time direction and (ii) the use of the theoretical isotopic distribution of an analyte as selection/exclusion criterion. The algorithm is integrated in the Lipid Data Analyzer (LDA) application which additionally provides standardization, a statistics module for results analysis, a batch mode for unattended analysis of several runs and a 3D viewer for the manual verification. The statistics module offers sample grouping, tests between sample groups and export functionalities, where the results are visualized by heat maps and bar charts. The presented algorithm has been applied to data from a controlled experiment and to biological data, containing analytes distributed over an intensity range of 10(6). Our approach shows improved sensitivity and an extremely high positive predictive value compared with existing methods. Consequently, the novel algorithm, integrated in a user-friendly application, is a valuable improvement in the high-throughput analysis of the lipidome. IMPLEMENTATION AND AVAILABILITY The Java application is freely available for non-commercial users at http://genome.tugraz.at/lda. Raw data associated with this manuscript may be downloaded from ProteomeCommons.org Tranche using the following hash: ZBh3nS5bXk6I/Vn32tB5Vh0qnMpVIW71HByFFQqM0RmdF4/4Hcn H3Wggh9kU2teYVOtM1JWwHIeMHqSS/bc2yYNFmyUAAAAAAACl DQ ==
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Affiliation(s)
- Jürgen Hartler
- Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria
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Ubaida Mohien C, Hartler J, Breitwieser F, Rix U, Remsing Rix L, Winter GE, Thallinger GG, Bennett KL, Superti-Furga G, Trajanoski Z, Colinge J. MASPECTRAS 2: An integration and analysis platform for proteomic data. Proteomics 2010; 10:2719-22. [PMID: 20455215 DOI: 10.1002/pmic.201000075] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
MASPECTRAS 2 is a freely available platform for integrating MS protein identifications with information from the major bioinformatics databases (ontologies, domains, literature, etc.). It assists researchers in understanding their data and publishing through sample comparisons, targeted queries, summaries, and exports in multiple formats such as PRIDE XML (Jones et al., Nucleic Acids Res. 2008, 36, D878-D883). MASPECTRAS 2 also comprises mechanisms to facilitate its integration in a high-throughput infrastructure. We illustrate application of MASPECTRAS 2 with unpublished tyrosine kinase inhibitor drug proteomics profiles in cancerous cells.
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Mlecnik B, Scheideler M, Hackl H, Hartler J, Sanchez-Cabo F, Trajanoski Z. PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways. Nucleic Acids Res 2005; 33:W633-7. [PMID: 15980551 PMCID: PMC1160152 DOI: 10.1093/nar/gki391] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
While generation of high-throughput expression data is becoming routine, the fast, easy, and systematic presentation and analysis of these data in a biological context is still an obstacle. To address this need, we have developed PathwayExplorer, which maps expression profiles of genes or proteins simultaneously onto major, currently available regulatory, metabolic and cellular pathways from KEGG, BioCarta and GenMAPP. PathwayExplorer is a platform-independent web server application with an optional standalone Java application using a SOAP (simple object access protocol) interface. Mapped pathways are ranked for the easy selection of the pathway of interest, displaying all available genes of this pathway with their expression profiles in a selectable and intuitive color code. Pathway maps produced can be downloaded as PNG, JPG or as high-resolution vector graphics SVG. The web service is freely available at https://pathwayexplorer.genome.tugraz.at; the standalone client can be downloaded at http://genome.tugraz.at.
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Affiliation(s)
| | | | | | | | | | - Zlatko Trajanoski
- To whom correspondence should be addressed. Tel: +43 316 873 5332; Fax: +43 316 873 5340;
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