Determines the validity of peptide identification by calculating p-values from tandem mass spectra (MS/MS). MS-GF can be used in addition to the decoy searches or on its own. The software can also generate a list of all peptides whose score exceeds a threshold and match these in a protein database.
A search engine independent platform for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics data.
Provides extension points to enable built-in import capabilities for binary or textual instrument vendors’ data formats. OpenChrom is an extensible cross-platform open source software for the mass spectrometric analysis of chromatographic data. This application offers extension points that enable the implementation of different baseline detectors as well as peak detectors and integrators. An option to implement filters, used to increase the chromatographic quality, is also available.
Permits users to import, integrate, manage and compare numerous proteomics datasets at the same time. PACOM is a Java standalone tool that provides an innovative, easy-to-use and powerful way of data comparison, generating a lot of different charts with protein and peptide features. This method offers a rich set of graphical representation of the most common proteomics data features.