Computational protocol: Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas

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Protocol publication

[…] Some of the process level details of the experiment processing are provided here. The mzXML [] conversions from vendor format files to mzXML files were performed using software available at our Sashimi software site []. The SEQUEST parameters used in MS/MS assignment were for semi-tryptic digestion and one static modification of methionine due to oxidation. Additional parameters were required for some datasets, such as those labeled with ICAT or samples treated with iodoacetemide. All sequest.params files can be found in the searched archive files at our repository [] for the public datasets. (Datasets that researchers have requested to be kept as private until they have published are not present in the data repository, but are included in the PeptideAtlas database with minimum sample annotation.)The PeptideProphet software is available at our Sashimi software site []. The SBEAMS database application and the Proteomics module and PeptideAtlas modules within it are available at our SBEAMS software site [] as downloads from a subversion code repository. The code is browsable from the worldwide web []. The BLAST algorithm was used with the parameters for 100% identity matches to a small peptide in a protein reference database:blastp -F F -W 2 -M PAM30 -G 9 -E 1 -e 10 -K 50 -b 50 […]

Pipeline specifications

Software tools Comet, PeptideProphet, SBEAMS, BLASTP
Databases PeptideAtlas
Application MS-based untargeted proteomics
Organisms Saccharomyces cerevisiae