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

Jemma X. Wu, Dana Pascovici, Vera Ignjatovic, Xiaomin Song, Christoph Krisp, Mark P. Molloy*

*Corresponding author for this work

Research output: Contribution to journalArticle

4 Citations (Scopus)

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.

Original languageEnglish
Article number1700174
Pages (from-to)1-5
Number of pages5
JournalProteomics
Volume17
Issue number19
DOIs
Publication statusPublished - 9 Oct 2017

Keywords

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

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