OMSSA pipeline

OMSSA specifications


Unique identifier OMICS_19842
Alternative 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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Publication for Open mass spectrometry search algorithm

OMSSA IN pipelines

PMCID: 4549250
PMID: 26305100
DOI: 10.1371/journal.ppat.1005128

[…] 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: 3759844
PMID: 23470796
DOI: 10.1016/j.jprot.2013.02.022

[…] a feature comparison of software used in recent publications for the quantitation of isobarically tagged ptm experiments. the coon group has developed the compass [32] proteomics analysis suite for omssa, used recently for the quantitation of stem cell proteomes and phosphoproteomes [18]. the marto group introduced multiplierz [33] that provides an excellent basis for extensible workflows […]

PMCID: 3430228
PMID: 22942697
DOI: 10.3390/ijms13078171

[…] (version, pacific northwest national laboratory (pnl)), dtarefinery (version 1.1, pnl) and dtatexttomgf (version 1.2.3952, pnl) to produce mgf files. sequence assignment was performed using omssa ms/ms search engine [70] (version 2.1.9, national center for biotechnology information (ncbi)) against the mouse international protein index (ipi) protein sequence database (version 3.52) [71] […]

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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