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DataSet Summary

  • HostingRepository: PRIDE
  • AnnounceDate: 2017-06-20
  • AnnouncementXML: Submission_2017-08-28_02:47:33.xml
  • DigitalObjectIdentifier:
  • ReviewLevel: Peer-reviewed dataset
  • DatasetOrigin: Original data
  • RepositorySupport: Unsupported dataset by repository
  • PrimarySubmitter: Ben Collins
  • Title: Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry
  • Description: Quantitative proteomics employing mass spectrometry has become an indispensable tool in basic and applied life science research. Methods based on data-dependent acquisition have proved extremely valuable for qualitative proteome analysis but historically have struggled to achieve reproducible quantitative data. Targeted proteomics, most commonly implemented as selected reaction monitoring, has emerged as a powerful alternative and succeeded in providing a data independent approach for reproducible quantitative proteomics data but is limited in the number of proteins quantified. SWATH-MS is a recently introduced implementation of the data-independent acquisition strategy that aims to maintain the favorable quantitative characteristics (accuracy, sensitivity, specificity) achieved in targeted proteomics but on the scale of thousands of proteins. While previous SWATH-MS studies have shown high intra-lab reproducibility, this has not been evaluated on an inter-lab basis. In this multi-laboratory evaluation study using data from 11 sites worldwide, we have demonstrated that using SWATH-MS we can consistently detect and quantify more than 4,000 proteins from HEK293 cells and that the quantitative protein data generated across laboratories is reproducible. Using synthetic peptide dilution series, we have shown that the sensitivity, dynamic range and reproducibility established with SWATH-MS methods are also uniformly achieved across labs. This study demonstrates that SWATH-MS is a reproducible technique that can be confidently deployed for large-scale protein quantification in life science research
  • SpeciesList: scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
  • ModificationList: monohydroxylated residue; iodoacetamide derivatized residue
  • Instrument: TripleTOF 5600

Dataset History

VersionDatetimeStatusChangeLog Entry
02016-08-23 02:00:04ID requested
12017-05-19 02:41:55announced
22017-06-20 05:44:47announcedUpdated project metadata.
32017-08-28 02:47:34announcedUpdated project metadata.

Publication List

  1. Collins BC, Hunter CL, Liu Y, Schilling B, Rosenberger G, Bader SL, Chan DW, Gibson BW, Gingras AC, Held JM, Hirayama-Kurogi M, Hou G, Krisp C, Larsen B, Lin L, Liu S, Molloy MP, Moritz RL, Ohtsuki S, Schlapbach R, Selevsek N, Thomas SN, Tzeng SC, Zhang H, Aebersold R, Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry. Nat Commun, 8(1):291(2017) [pubmed]

Keyword List

  1. curator keyword: Technical
  2. submitter keyword: SWATH-MS, reproducibility, proteomics

Contact List

    Ruedi Aebersold
    • contact affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
    • contact email: aebersold@imsb.biol.ethz.ch
    • lab head:
    Ben Collins
    • contact affiliation: ETH Zurich
    • contact email: collins@imsb.biol.ethz.ch
    • dataset submitter:

Full Dataset Link List

  1. Dataset FTP location
  2. PRIDE project URI
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