Open mass spectrometry search algorithm.
Large numbers of MS/MS peptide spectra generated in proteomics experiments require efficient, sensitive and specific algorithms for peptide identification. In the Open Mass Spectrometry Search Algorithm (OMSSA), specificity is calculated by a classic probability score using an explicit model for matching experimental spectra to sequences. At default thresholds, OMSSA matches more spectra from a standard protein cocktail than a comparable algorithm. OMSSA is designed to be faster than published algorithms in searching large MS/MS datasets.
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA. lewisg@mail.nih.gov
Lewis Y
LY
Geer
Sanford P
SP
Markey
Jeffrey A
JA
Kowalak
Lukas
L
Wagner
Ming
M
Xu
Dawn M
DM
Maynard
Xiaoyu
X
Yang
Wenyao
W
Shi
Stephen H
SH
Bryant
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D005189:False Positive Reactions; D013058:Mass Spectrometry / Q000379:methods; D010446:Peptide Fragments / Q000032:analysis; D016012:Poisson Distribution; D011506:Proteins / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D012372:ROC Curve; D015203:Reproducibility of Results
D010446:Peptide Fragments; D011506:Proteins