Dataset Information

Building high-quality assay libraries for targeted analysis of SWATH MS data

ABSTRACT: Targeted proteomics by selected/multiple reaction monitoring or, on a larger scale, by SWATH MS relies on spectral reference libraries for peptide identification. Quality and coverage of these libraries are therefore of critical importance. Here we present a detailed protocol that has been successfully used to build high-quality, extensive reference libraries supporting targeted proteomics by SWATH MS. We describe each step of the process, including data acquisition by discovery proteomics, assertion of peptide-spectrum matches, generation of consensus spectra and compilation of mass spectrometric coordinates that uniquely define each targeted peptide. Crucial steps of this process such as FDR control, retention time normalization and handling of post-translationally modified peptides are discussed in detail. Finally we show how to use the library to extract SWATH data with the open-source software Skyline. The protocol takes 2-3 days to complete, depending on the extent of the library and the computational resources available.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Saccharomyces Cerevisiae (ncbitaxon:4932)

SUBMITTER: Ruedi Aebersold

PROVIDER: MSV000082506 | MassIVE | Tue Jun 26 14:17:00 BST 2018

SECONDARY ACCESSION(S): PXD001126

REPOSITORIES: MassIVE

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Building high-quality assay libraries for targeted analysis of SWATH MS data.

Schubert Olga T OT Gillet Ludovic C LC Collins Ben C BC Navarro Pedro P Rosenberger George G Wolski Witold E WE Lam Henry H Amodei Dario D Mallick Parag P MacLean Brendan B Aebersold Ruedi R

Nature protocols 20150212 3

Targeted proteomics by selected/multiple reaction monitoring (S/MRM) or, on a larger scale, by SWATH (sequential window acquisition of all theoretical spectra) MS (mass spectrometry) typically relies on spectral reference libraries for peptide identification. Quality and coverage of these libraries are therefore of crucial importance for the performance of the methods. Here we present a detailed protocol that has been successfully used to build high-quality, extensive reference libraries support ...[more]

PMID: 25675208

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