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epic for Proteomicsepic: Estimating Peptide Identification Confidence can estimate p- and q-values along with False Discovery Rates (FDR) for bottom-up proteomics experiments involving tandem mass spectrometry. This is achieved by transforming the original scores from peptide search engines such as Sequest, X!Tandem, and Spectrum Mill, to a form that separates true and random hits and fitting a mixture of multivariate Gaussian models to them. This work extends the approach by PeptideProphet. Inp
PeptideProphet and ProteinProphet CGI program source files modified to make interoperable with Rosetta Biosoftware's Elucidator(R) System. All files are published and distributed under the LGPL license, v2.1.
BiblioSpec is a suite of tools for creating, managing, and searching MS/MS spectrum libraries. Libraries can be built from database search results in a variety of formats (e.g. .pep.xml files from PeptideProphet, part of the TPP). A redundant library can be filtered down to one example spectrum for each peptide sequence at each charge state. The libraries can be searched to find petpide identifications for new spectra. Libraries are stored as sqlite3 files. The BiblioSpec interface is command li