MassMatrix: A database search program for rapid characterization of proteins and peptides from tandem mass spectrometry data |
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Authors: | Hua Xu Michael A Freitas Dr |
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Institution: | 1. Department of Chemistry, The Ohio State University, Columbus, OH, USA;2. Department of Molecular Immunology Virology and Medical Genetics, The Ohio State University, Columbus, OH, USA |
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Abstract: | MassMatrix is a program that matches tandem mass spectra with theoretical peptide sequences derived from a protein database. The program uses a mass accuracy sensitive probabilistic score model to rank peptide matches. The MS/MS search software was evaluated by use of a high mass accuracy dataset and its results compared with those from MASCOT, SEQUEST, X!Tandem, and OMSSA. For the high mass accuracy data, MassMatrix provided better sensitivity than MASCOT, SEQUEST, X!Tandem, and OMSSA for a given specificity and the percentage of false positives was 2%. More importantly all manually validated true positives corresponded to a unique peptide/spectrum match. The presence of decoy sequence and additional variable PTMs did not significantly affect the results from the high mass accuracy search. MassMatrix performs well when compared with MASCOT, SEQUEST, X!Tandem, and OMSSA with regard to search time. MassMatrix was also run on a distributed memory clusters and achieved search speeds of ~100 000 spectra per hour when searching against a complete human database with eight variable modifications. The algorithm is available for public searches at http://www.massmatrix.net. |
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Keywords: | Database search High mass accuracy Post‐translational modification Tandem mass spectra |
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