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PXD001126

PXD001126 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleBuilding high-quality assay libraries for targeted analysis of SWATH MS data
DescriptionTargeted 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.
HostingRepositoryPRIDE
AnnounceDate2015-01-26
AnnouncementXMLSubmission_2015-03-16_07:48:26.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterBen Collins
SpeciesList scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentTripleTOF 5600
Dataset History
RevisionDatetimeStatusChangeLog Entry
02014-07-10 07:56:34ID requested
12015-01-26 02:00:55announced
22015-03-16 07:48:27announcedUpdated publication reference for PubMed record(s): 25675208.
Publication List
Schubert OT, Gillet LC, Collins BC, Navarro P, Rosenberger G, Wolski WE, Lam H, Amodei D, Mallick P, MacLean B, Aebersold R, Building high-quality assay libraries for targeted analysis of SWATH MS data. Nat Protoc, 10(3):426-41(2015) [pubmed]
Keyword List
curator keyword: Biological
submitter keyword: SWATH, spectral library, assay library, yeast
Contact List
Ruedi Aebersold
contact affiliationInstitute of Molecular Systems Biology ETH Zürich Switzerland
contact emailaebersold@imsb.biol.ethz.ch
lab head
Ben Collins
contact affiliationETH Zurich
contact emailcollins@imsb.biol.ethz.ch
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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