OMSSA specifications


Unique identifier OMICS_19842
Name Open mass spectrometry search algorithm
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A dta file format and a generic file format.
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained No



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OMSSA article

OMSSA citations

PMCID: 5821407

[…] library build available from at the time of searching was used. cmn files were searched using x!tandem using both the native and k-score scoring algorithms. mgf files were searched using omssa with precursor mass tolerance settings of +/- 20 ppm, product ions mass tolerance of +/- 1.5 da, and fragment settings of +/- 0.5 da [17]. xml output files were parsed using masssieve (nih). […]

PMCID: 4549250

[…] files were analyzed using the central proteomics facilities pipeline (cpfp), version 2.1.0 [46,47]. peptide identification was performed using the x!tandem [48] and open ms search algorithm (omssa) [49] search engines against a database consisting of v. alginolyticus 12g01 sequences from uniprot knowledgebase, with common contaminants and reversed decoy sequences appended [50]. fragment […]

PMCID: 1933459

[…] data (see text s3 and text s5)., phenyx is freely available at and mascot at two open-source database search engines have been developed, omssa [61] and x!tandem [62]. several public ms/ms data repositories are accessible over the internet, including peptide atlas (, open proteomics database […]

OMSSA institution(s)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurotoxicology, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
OMSSA funding source(s)
Supported by the NIH intramural research program.

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