PXD001126 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Building high-quality assay libraries for targeted analysis of SWATH MS data |
Description | 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. |
HostingRepository | PRIDE |
AnnounceDate | 2015-01-26 |
AnnouncementXML | Submission_2015-03-16_07:48:26.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Ben Collins |
SpeciesList | scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932; |
ModificationList | monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | TripleTOF 5600 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2014-07-10 07:56:34 | ID requested | |
1 | 2015-01-26 02:00:55 | announced | |
⏵ 2 | 2015-03-16 07:48:27 | announced | Updated 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 affiliation | Institute of Molecular Systems Biology ETH Zürich Switzerland |
contact email | aebersold@imsb.biol.ethz.ch |
lab head | |
Ben Collins |
contact affiliation | ETH Zurich |
contact email | collins@imsb.biol.ethz.ch |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD001126
- Label: PRIDE project
- Name: Building high-quality assay libraries for targeted analysis of SWATH MS data