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PMID: 19235167 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

MassMatrix: a database search program for rapid characterization of proteins and peptides from tandem mass spectrometry data.

Proteomics ·Vol. 9 ·No. 6 ·2009-03-00 ·Pages 1548-55

Xu H, Freitas MA

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 approximately 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).

MeSH Terms
Algorithms Databases, Protein False Positive Reactions Humans Molecular Weight Peptides/analysis,chemistry Proteins/analysis ROC Curve Software Tandem Mass Spectrometry
Chemicals
Peptides Proteins
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Xu Hua
Department of Chemistry, The Ohio State University, Columbus, OH 43210, USA.
Freitas Michael A
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Article Info
Journal
Proteomics
Abbr.
Proteomics
ISSN
1615-9861
DOI
10.1002/pmic.200700322
Published
2009-03-00
Pages
1548-55
Language
English
Region
Germany
NLM ID
101092707
PMCID
PMC2759086
Subset
IM
Grants
NCI NIH HHS · R01 CA107106 · United States
NCI NIH HHS · R01 CA107106-04 · United States
NCI NIH HHS · R56 CA107106 · United States
NCI NIH HHS · CA107106 · United States
External Links
PubMed source DOI: 10.1002/pmic.200700322 PMC Full Text View journal details
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