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MSFragger is an ultrafast database search tool for peptide identifications in mass spectrometry-based proteomics. It differs from conventional search engines by computing similarity scores in a fragment-centric fashion using a theoretical fragment index of candidate peptides. The speed of MSFragger makes it particularly suitable for ‘open’ database searches, where the precursor mass tolerance is set to hundreds of Daltons, for the identification of modified peptides. MSFragger is implemented in the cross-platform Java programming language and is compatible with standard proteomics file formats such as MGF/mzXML/mzML/pepXML.