Mascot is a powerful search engine which uses mass spectrometry data to identify proteins from primary sequence databases. Mascot integrates all of the proven methods of searching: Peptide Mass Fingerprint (the only experimental data are peptide mass values), Sequence Query (peptide mass data are combined with amino acid sequence and composition information), MS/MS Ion Search using uninterpreted MS/MS data from one or more peptides.
MzJava is an open-source Java library for the analysis of mass spectrometry data. It provides algorithms and data structures for processing mass spectra and their associated biological molecules, such as small molecules, glycans, proteins, and peptides with post-translational modifications. MzJava includes methods to perform mass calculation, protein digestion, peptide and glycan fragmentation, MS/MS signal processing, and scoring for spectra-spectra and peptide/glycan-spectra matches.
PepFrag is a tool for identifying proteins from a collection of sequences that matches a single tandem mass spectrum.
Proteomics tools for mining sequence databases in conjunction with mass spectrometry experiments, including MS-Fit, MS-Pattern, MS-Digest, etc.
QuickMod is a spectral library search based MSMS data analysis tool, designed to identify modified peptides. The QuickMod algorithm assumes that the precursor mass difference between a query spectrum and a candidate library spectrum can be explained by a modification. Based on this assumption the two spectra are aligned and the fit of the spectral alignment is assigned a similarity score. In a second step the most likely attachment position of the modification is determined.
Computes all possible crosslinks based on proteins of interest (max. 30 proteins) for further interrogation using standard search engine (e.g. Phenyx, Mascot, Sequest, OMSSA, X!Tandem)
xQuest is a search engine for cross-linked peptides from complex samples. xQuest works with small and large protein databases and features flexible fragment ion assignment, advanced scoring, and interactive evaluation tools.