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Improving Protein Detection Confidence Using SWATH-Mass Spectrometry with Large Peptide Reference Libraries

2017; Wiley; Volume: 17; Issue: 19 Linguagem: Inglês

10.1002/pmic.201700174

1615-9861

Jemma Wu, Dana Pascovici, Vera Ignjatović, Xiaomin Song, Christoph Krisp, Mark P. Molloy,

Metabolomics and Mass Spectrometry Studies

PROTEOMICSVolume 17, Issue 19 1700174 TECHNICAL BRIEF Improving Protein Detection Confidence Using SWATH-Mass Spectrometry with Large Peptide Reference Libraries Jemma X. Wu, Jemma X. Wu Australian Proteome Analysis Facility (APAF), Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, AustraliaSearch for more papers by this authorDana Pascovici, Dana Pascovici Australian Proteome Analysis Facility (APAF), Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, AustraliaSearch for more papers by this authorVera Ignjatovic, Vera Ignjatovic Hematology Research Laboratory, Murdoch Children's Research Institute, Melbourne, AustraliaSearch for more papers by this authorXiaomin Song, Xiaomin Song Australian Proteome Analysis Facility (APAF), Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, AustraliaSearch for more papers by this authorChristoph Krisp, Christoph Krisp Australian Proteome Analysis Facility (APAF), Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, AustraliaSearch for more papers by this authorMark P. Molloy, Corresponding Author Mark P. Molloy mmolloy@proteome.org.au Australian Proteome Analysis Facility (APAF), Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia Associate Professor, Mark P. Molloy, Australian Proteome Analysis Facility (APAF), Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia E-mail: mmolloy@proteome.org.auSearch for more papers by this author Jemma X. Wu, Jemma X. Wu Australian Proteome Analysis Facility (APAF), Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, AustraliaSearch for more papers by this authorDana Pascovici, Dana Pascovici Australian Proteome Analysis Facility (APAF), Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, AustraliaSearch for more papers by this authorVera Ignjatovic, Vera Ignjatovic Hematology Research Laboratory, Murdoch Children's Research Institute, Melbourne, AustraliaSearch for more papers by this authorXiaomin Song, Xiaomin Song Australian Proteome Analysis Facility (APAF), Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, AustraliaSearch for more papers by this authorChristoph Krisp, Christoph Krisp Australian Proteome Analysis Facility (APAF), Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, AustraliaSearch for more papers by this authorMark P. Molloy, Corresponding Author Mark P. Molloy mmolloy@proteome.org.au Australian Proteome Analysis Facility (APAF), Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia Associate Professor, Mark P. Molloy, Australian Proteome Analysis Facility (APAF), Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia E-mail: mmolloy@proteome.org.auSearch for more papers by this author First published: 18 August 2017 https://doi.org/10.1002/pmic.201700174Citations: 5Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat Abstract Protein quantification using data-independent acquisition methods such as SWATH-MS most commonly relies on spectral matching to a reference MS/MS assay library. To enable deep proteome coverage and efficient use of existing data, in silico approaches have been described to use archived or publicly available large reference spectral libraries for spectral matching. Since implicit in the use of larger libraries is the increasing likelihood of false-discoveries, new workflows are needed to ensure high confidence in protein matching under these conditions. We present a workflow which introduces a range of filters and thresholds aimed at increasing confidence that the resulting proteins are reliably detected and their quantitation is consistent and reproducible. We demonstrated the workflow using extended libraries with SWATH data from human plasma samples and yeast-spiked human K562 cell lysate digest. Citing Literature Supporting Information Filename Description pmic12723-sup-0001-SuppMat.docx1.6 MB Supplemental material Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article. Volume17, Issue19October 20171700174 RelatedInformation