Open Mass Spectrometry Search Algorithm

2004/06/01 by Lewis Y. Geer, Geer, Lewis Y., Sanford P. Markey +16
Biochemistry, Genetics and Molecular Biology · Chemistry · #Advanced Proteomics Techniques and Applications #FOS: Biological sciences #Mass Spectrometry Techniques and Applications #Metabolomics and Mass Spectrometry Studies #Quantitative Methods (q-bio.QM) #q-bio.QM

paper · pdf · doi:10.48550/arxiv.q-bio/0406002

arxiv created 2004/06/01 · openalex publication_date 2004/06/01 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28

Abstract

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.

Related

• Discovery of Proteomics based on Machine learning
• Peptide-Spectra Matching from Weak Supervision
• Mass spectrometry based protein identification with accurate statistical significance assignment
• End-to-end deep attention-based multitask pipeline for predicting uncertainty-quantified peptide properties from mass spectrometry data
• Efficient online learning for large-scale peptide identification