Swiss Institute of Bioinformatics

Popitam

Interface: latest update 5/02/2009
Popitam: version 4.0 (1/02/2009)

Popitam is a method designed to characterize peptides with mutations or unexpected post-translational modifications using MS/MS data. A short description of the algorithm can be found here (pdf document, about 2Mb).

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More about Popitam

			About the examples
Input data parameter Data file : Data file content : Data file format : mgf dta Other general parameters Database : UniProtKB/Swiss-Prot UniProtKB/TrEMBL Release 56.7 of 20-Jan-2009 Release 39.7 of 20-Jan-2009 decoy AC list (< 2000) : Required parameter. Instrument : TOFTOF QTOF Fragment error : Da Enzyme : AspN + LysC AspN + GluN + LysC Pepsin pH 1.3 Chymotrypsin High Pepsin pH > 2 Trypsin Proteinase K LysN AspN GluC bicarbonate Tryp + GluC CNBr LysC GluC phosphate AspN + GluN ArgC Chymotrypsin Low Tryp + Chymo Allow up to 1 0 missed cleavage Scoring function (facultative parameter) If nothing is specified, popitam will use its default scoring functions. Scoring file : Scoring file content : Open-modification search parameters modGap number : 1 2 Precursor mass range to Da modGap mass range to Da Output parameters Number of displayed peptides : Your E-mail address Please note that submissions are limited in time to 5 minutes. For longer jobs, please specify your e-mail address in the corresponding field, so that results can be sent.