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PMID: 25977788 Published · epublish English Dataset Journal Article Research Support, Non-U.S. Gov't

A repository of assays to quantify 10,000 human proteins by SWATH-MS.

Scientific data ·Vol. 1 ·2014-00-00 ·Pages 140031

Rosenberger G, Koh CC, Guo T, Röst HL, Kouvonen P, Collins BC, Heusel M, Liu Y, Caron E, Vichalkovski A, Faini M, Schubert OT, Faridi P, Ebhardt HA, Matondo M, Lam H, Bader SL, Campbell DS, Deutsch EW, Moritz RL, Tate S, Aebersold R

Abstract

Mass spectrometry is the method of choice for deep and reliable exploration of the (human) proteome. Targeted mass spectrometry reliably detects and quantifies pre-determined sets of proteins in a complex biological matrix and is used in studies that rely on the quantitatively accurate and reproducible measurement of proteins across multiple samples. It requires the one-time, a priori generation of a specific measurement assay for each targeted protein. SWATH-MS is a mass spectrometric method that combines data-independent acquisition (DIA) and targeted data analysis and vastly extends the throughput of proteins that can be targeted in a sample compared to selected reaction monitoring (SRM). Here we present a compendium of highly specific assays covering more than 10,000 human proteins and enabling their targeted analysis in SWATH-MS datasets acquired from research or clinical specimens. This resource supports the confident detection and quantification of 50.9% of all human proteins annotated by UniProtKB/Swiss-Prot and is therefore expected to find wide application in basic and clinical research. Data are available via ProteomeXchange (PXD000953-954) and SWATHAtlas (SAL00016-35).

MeSH Terms
Databases, Protein Humans Mass Spectrometry/methods Proteins/chemistry Proteome/chemistry Proteomics/methods
Chemicals
Proteins Proteome
Authors & Affiliations
22 authors, click to expand affiliations / ORCID
Rosenberger George
Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; PhD Program in Systems Biology, University of Zurich and ETH Zurich , CH-8093 Zurich, Switzerland.
Koh Ching Chiek
Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; Ruprecht Karls University of Heidelberg , DE-69117 Heidelberg, Germany.
Guo Tiannan
Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland.
Röst Hannes L
Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; PhD Program in Systems Biology, University of Zurich and ETH Zurich , CH-8093 Zurich, Switzerland.
Kouvonen Petri
Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland.
Collins Ben C
Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland.
Heusel Moritz
Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; PhD Program in Molecular and Translational Biomedicine, Competence Centre for Systems Physiology and Metabolic Diseases (CC-SPMD), University of Zurich and ETH Zurich , CH-8093 Zurich, Switzerland.
Liu Yansheng
Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland.
Caron Etienne
Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland.
Vichalkovski Anton
Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland.
Faini Marco
Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland.
Schubert Olga T
Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; PhD Program in Systems Biology, University of Zurich and ETH Zurich , CH-8093 Zurich, Switzerland.
Faridi Pouya
Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; Department of Phytopharmaceuticals (Traditional Pharmacy), School of Pharmacy and Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, 71345-1583 Shiraz, Iran.
Ebhardt H Alexander
Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland.
Matondo Mariette
Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland.
Lam Henry
Division of Biomedical Engineering and Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay , Hong Kong, China.
Bader Samuel L
Institute for Systems Biology , Seattle, Washington 98109-5234, USA.
Campbell David S
Institute for Systems Biology , Seattle, Washington 98109-5234, USA.
Deutsch Eric W
Institute for Systems Biology , Seattle, Washington 98109-5234, USA.
Moritz Robert L
Institute for Systems Biology , Seattle, Washington 98109-5234, USA.
Tate Stephen
AB SCIEX , Concord, Ontario L4K 4V8, Canada.
Aebersold Ruedi
Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; Faculty of Science, University of Zurich , CH-8057 Zurich, Switzerland.
References (62)
62 references, click to expand
  1. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.
    Anal Chem. 2002 Oct 15;74(20):5383-92 PMID: 12403597
  2. A method for reducing the time required to match protein sequences with tandem mass spectra.
    Rapid Commun Mass Spectrom. 2003;17(20):2310-6 PMID: 14558131
  3. Protein sequence databases.
    Curr Opin Chem Biol. 2004 Feb;8(1):76-80 PMID: 15036160
  4. Open mass spectrometry search algorithm.
    J Proteome Res. 2004 Sep-Oct;3(5):958-64 PMID: 15473683
  5. A uniform proteomics MS/MS analysis platform utilizing open XML file formats.
    Mol Syst Biol. 2005;1:2005.0017 PMID: 16729052
  6. General framework for developing and evaluating database scoring algorithms using the TANDEM search engine.
    Bioinformatics. 2006 Nov 15;22(22):2830-2 PMID: 16877754
  7. MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis.
    J Proteome Res. 2007 Feb;6(2):654-61 PMID: 17269722
  8. Development and validation of a spectral library searching method for peptide identification from MS/MS.
    Proteomics. 2007 Mar;7(5):655-67 PMID: 17295354
  9. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry.
    Nat Methods. 2007 Mar;4(3):207-14 PMID: 17327847
  10. Tricine-SDS-PAGE.
    Nat Protoc. 2006;1(1):16-22 PMID: 17406207
  11. In-gel digestion for mass spectrometric characterization of proteins and proteomes.
    Nat Protoc. 2006;1(6):2856-60 PMID: 17406544
  12. Building consensus spectral libraries for peptide identification in proteomics.
    Nat Methods. 2008 Oct;5(10):873-5 PMID: 18806791
  13. An integrated workflow for charting the human interaction proteome: insights into the PP2A system.
    Mol Syst Biol. 2009;5:237 PMID: 19156129
  14. A HUPO test sample study reveals common problems in mass spectrometry-based proteomics.
    Nat Methods. 2009 Jun;6(6):423-30 PMID: 19448641
  15. Unique ion signature mass spectrometry, a deterministic method to assign peptide identity.
    Mol Cell Proteomics. 2009 Sep;8(9):2051-62 PMID: 19556279
  16. Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry.
    Mol Cell Proteomics. 2009 Nov;8(11):2405-17 PMID: 19608599
  17. Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses.
    Mol Cell Proteomics. 2010 Feb;9(2):225-41 PMID: 19837981
  18. Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome.
    J Proteome Res. 2009 Dec;8(12):5674-8 PMID: 19848406
  19. Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance.
    Mol Cell Proteomics. 2010 Feb;9(2):242-54 PMID: 19858499
  20. Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry.
    J Proteome Res. 2010 Feb 5;9(2):761-76 PMID: 19921851
  21. High-throughput generation of selected reaction-monitoring assays for proteins and proteomes.
    Nat Methods. 2010 Jan;7(1):43-6 PMID: 19966807
  22. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments.
    Bioinformatics. 2010 Apr 1;26(7):966-8 PMID: 20147306
  23. Options and considerations when selecting a quantitative proteomics strategy.
    Nat Biotechnol. 2010 Jul;28(7):710-21 PMID: 20622845
  24. Towards a knowledge-based Human Protein Atlas.
    Nat Biotechnol. 2010 Dec;28(12):1248-50 PMID: 21139605
  25. Too many roads not taken.
    Nature. 2011 Feb 10;470(7333):163-5 PMID: 21307913
  26. mProphet: automated data processing and statistical validation for large-scale SRM experiments.
    Nat Methods. 2011 May;8(5):430-5 PMID: 21423193
  27. UniProt Knowledgebase: a hub of integrated protein data.
    Database (Oxford). 2011 Mar 29;2011:bar009 PMID: 21447597
  28. Improving SRM assay development: a global comparison between triple quadrupole, ion trap, and higher energy CID peptide fragmentation spectra.
    J Proteome Res. 2011 Sep 2;10(9):4334-41 PMID: 21726076
  29. iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates.
    Mol Cell Proteomics. 2011 Dec;10(12):M111.007690 PMID: 21876204
  30. Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets.
    Proteomics. 2011 Nov;11(22):4434-8 PMID: 21932440
  31. The quantitative proteome of a human cell line.
    Mol Syst Biol. 2011 Nov 08;7:549 PMID: 22068332
  32. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis.
    Mol Cell Proteomics. 2012 Jun;11(6):O111.016717 PMID: 22261725
  33. Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins.
    Mol Cell Proteomics. 2012 Mar;11(3):M111.014050 PMID: 22278370
  34. Modification site localization scoring: strategies and performance.
    Mol Cell Proteomics. 2012 May;11(5):3-14 PMID: 22328712
  35. A computational tool to detect and avoid redundancy in selected reaction monitoring.
    Mol Cell Proteomics. 2012 Aug;11(8):540-9 PMID: 22535207
  36. Using iRT, a normalized retention time for more targeted measurement of peptides.
    Proteomics. 2012 Apr;12(8):1111-21 PMID: 22577012
  37. Inference and validation of protein identifications.
    Mol Cell Proteomics. 2012 Nov;11(11):1097-104 PMID: 22865921
  38. Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics.
    Mol Cell Proteomics. 2012 Nov;11(11):1475-88 PMID: 22865924
  39. The first comprehensive and quantitative analysis of human platelet protein composition allows the comparative analysis of structural and functional pathways.
    Blood. 2012 Oct 11;120(15):e73-82 PMID: 22869793
  40. Comet: an open-source MS/MS sequence database search tool.
    Proteomics. 2013 Jan;13(1):22-4 PMID: 23148064
  41. The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013.
    Nucleic Acids Res. 2013 Jan;41(Database issue):D1063-9 PMID: 23203882
  42. Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes.
    Nat Commun. 2012;3:1301 PMID: 23250431
  43. A first step toward completion of a genome-wide characterization of the human proteome.
    J Proteome Res. 2013 Jan 4;12(1):1-5 PMID: 23256439
  44. The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community.
    J Proteome Res. 2013 Jan 4;12(1):23-7 PMID: 23259511
  45. Proteomics meets the scientific method.
    Nat Methods. 2013 Jan;10(1):24-7 PMID: 23269373
  46. Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS.
    Proteomics. 2013 Apr;13(8):1247-56 PMID: 23322582
  47. A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis.
    Nature. 2013 Feb 14;494(7436):266-70 PMID: 23334424
  48. The Mtb proteome library: a resource of assays to quantify the complete proteome of Mycobacterium tuberculosis.
    Cell Host Microbe. 2013 May 15;13(5):602-612 PMID: 23684311
  49. Finding the right antibody for the job.
    Nat Methods. 2013 Jul 30;10(8):703-7 PMID: 23900250
  50. Global proteome analysis of the NCI-60 cell line panel.
    Cell Rep. 2013 Aug 15;4(3):609-20 PMID: 23933261
  51. Protein synthesis rate is the predominant regulator of protein expression during differentiation.
    Mol Syst Biol. 2013;9:689 PMID: 24045637
  52. Mass spectrometric protein maps for biomarker discovery and clinical research.
    Expert Rev Mol Diagn. 2013 Nov;13(8):811-25 PMID: 24138574
  53. The strategy, organization, and progress of the HUPO Human Proteome Project.
    J Proteomics. 2014 Apr 4;100:3-7 PMID: 24145142
  54. Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition.
    Nat Methods. 2013 Dec;10(12):1239-45 PMID: 24162924
  55. Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system.
    Nat Methods. 2013 Dec;10(12):1246-53 PMID: 24162925
  56. State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project.
    J Proteome Res. 2014 Jan 3;13(1):60-75 PMID: 24261998
  57. Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins.
    J Proteome Res. 2014 Jan 3;13(1):15-20 PMID: 24364385
  58. Conserved peptide fragmentation as a benchmarking tool for mass spectrometers and a discriminating feature for targeted proteomics.
    Mol Cell Proteomics. 2014 Aug;13(8):2056-71 PMID: 24623587
  59. OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data.
    Nat Biotechnol. 2014 Mar;32(3):219-23 PMID: 24727770
  60. ProteomeXchange provides globally coordinated proteomics data submission and dissemination.
    Nat Biotechnol. 2014 Mar;32(3):223-6 PMID: 24727771
  61. A draft map of the human proteome.
    Nature. 2014 May 29;509(7502):575-81 PMID: 24870542
  62. Mass-spectrometry-based draft of the human proteome.
    Nature. 2014 May 29;509(7502):582-7 PMID: 24870543
Article Info
Journal
Scientific data
Abbr.
Sci Data
ISSN
2052-4463
DOI
10.1038/sdata.2014.31
Published
2014-00-00
Epub
2014-00-16
Pages
140031
Language
English
Region
England
NLM ID
101640192
PMCID
PMC4322573
Subset
IM
Grants
NIGMS NIH HHS · P50 GM076547 · United States
NIGMS NIH HHS · R01 GM087221 · United States
NHGRI NIH HHS · RC2 HG005805 · United States
NCRR NIH HHS · S10 RR027584 · United States
External Links
PubMed source DOI: 10.1038/sdata.2014.31 PMC Full Text View journal details
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