Improving protein detection confidence using SWATH-Mass spectrometry with large peptide reference libraries

Research output: Contribution to journalArticleResearchpeer-review

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.

LanguageEnglish
Article number1700174
Pages1-5
Number of pages5
JournalProteomics
Volume17
Issue number19
DOIs
Publication statusPublished - 9 Oct 2017

Fingerprint

Peptide Library
Libraries
Mass spectrometry
Workflow
Mass Spectrometry
Proteins
Plasma (human)
K562 Cells
Proteome
Computer Simulation
Yeast
Assays
Yeasts

Keywords

  • false-discovery rate
  • quantification
  • spectral library
  • SWATH

Cite this

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title = "Improving protein detection confidence using SWATH-Mass spectrometry with large peptide reference libraries",
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.",
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Improving protein detection confidence using SWATH-Mass spectrometry with large peptide reference libraries. / Wu, Jemma X.; Pascovici, Dana; Ignjatovic, Vera; Song, Xiaomin; Krisp, Christoph; Molloy, Mark P.

In: Proteomics, Vol. 17, No. 19, 1700174, 09.10.2017, p. 1-5.

Research output: Contribution to journalArticleResearchpeer-review

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AU - Wu, Jemma X.

AU - Pascovici, Dana

AU - Ignjatovic, Vera

AU - Song, Xiaomin

AU - Krisp, Christoph

AU - Molloy, Mark P.

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