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 mat...

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Veröffentlicht in:	Journal of proteome research 2004-09, Vol.3 (5), p.958-964
Hauptverfasser:	Geer, Lewis Y, Markey, Sanford P, Kowalak, Jeffrey A, Wagner, Lukas, Xu, Ming, Maynard, Dawn M, Yang, Xiaoyu, Shi, Wenyao, Bryant, Stephen H
Format:	Artikel
Sprache:	eng
Schlagworte:	Algorithms Computational Biology - methods Databases, Protein False Positive Reactions Mass Spectrometry - methods Peptide Fragments - analysis Poisson Distribution Proteins - analysis Proteomics - methods Reproducibility of Results ROC Curve
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Beschreibung
Zusammenfassung:	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. Keywords: protein identification • algorithm • bioinformatics • mass spectrometry • proteomics • significance testing
ISSN:	1535-3893 1535-3907
DOI:	10.1021/pr0499491