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Protocols

OMSSA specifications

Information


Unique identifier OMICS_19842
Name OMSSA
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 No
Maintained No

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Publication for Open mass spectrometry search algorithm

OMSSA citations

 (232)
library_books

Identification of a unique Radical SAM methyltransferase required for the sp3 C methylation of an arginine residue of methyl coenzyme M reductase

2018
Sci Rep
PMCID: 5943407
PMID: 29743535
DOI: 10.1038/s41598-018-25716-x

[…] The raw mass spectrometric data were converted to mgf-files using MSConvert. SearchGUI software (v3.2.17) and the OMSSA search engine were used for peptide identification. The data were searched against the M. acetivorans proteome database obtained from UniProt (Taxon identifier 188937). Through ETciD fragmentati […]

call_split

Hookworm Secreted Extracellular Vesicles Interact With Host Cells and Prevent Inducible Colitis in Mice

2018
Front Immunol
PMCID: 5936971
PMID: 29760697
DOI: 10.3389/fimmu.2018.00850
call_split See protocol

[…] e (PRJEB511) with the common repository of adventitious proteins (cRAP) appended to it. Database search was performed using Mascot Versions 2.4 (Matrix Science Ltd., London, UK) and X!Tandem, MS-GF+, OMSSA, and Tide search engines using SearchGUI (). The same parameters were used as described in Ref. ().The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium via […]

library_books

Proteomic analysis of corneal endothelial cell descemet membrane tissues reveals influence of insulin dependence and disease severity in type 2 diabetes mellitus

2018
PLoS One
PMCID: 5846724
PMID: 29529022
DOI: 10.1371/journal.pone.0192287

[…] ethionine oxidation, and protein-level expectation value scores of 0.0001 or lower. MGF files were searched using the most recent protein sequence libraries available from UniProtKB, X!Tandem [], and OMSSA []. […]

library_books

Elongator and codon bias regulate protein levels in mammalian peripheral neurons

2018
Nat Commun
PMCID: 5832791
PMID: 29497044
DOI: 10.1038/s41467-018-03221-z

[…] uence library. MGF files were searched using X!!Tandem (10.1021/pr0701198) using both the native (10.1093/bioinformatics/bth092) and k-score (10.1093/bioinformatics/btl379) scoring algorithms, and by OMSSA (10.1021/pr0499491). All searches were performed on Amazon Web Services-based cluster compute instances using the Proteome Cluster interface. XML output files were parsed and non-redundant prote […]

library_books

Proteomic analysis of the human retina reveals region specific susceptibilities to metabolic and oxidative stress related diseases

2018
PLoS One
PMCID: 5821407
PMID: 29466423
DOI: 10.1371/journal.pone.0193250

[…] nverted to .MGF format and then to .CMN format using msconvert and common. Detailed search parameters are printed in the output data files. Peak list data were searched using three algorithms: NCBI’s OMSSA[] and The GPM’s X!Tandem,[] and X!Hunter.[] The Ensembl human protein sequence library (version 37, reviewed) was used in a target-decoy format. For X!Hunter the latest library build available f […]

library_books

Dysregulation of fibulin 5 and matrix metalloproteases in epithelial ovarian cancer

2018
Oncotarget
PMCID: 5865667
PMID: 29581841
DOI: 10.18632/oncotarget.24484

[…] st format and analyzed using the central proteomics facilities pipeline (CPFP), version 2.0.3 [, ]. Peptide identification was performed using a non-specific search with the open MS search algorithm (OMSSA) [] against the appropriate protein database from Uniprot, with common contaminants and reversed decoy sequences appended []. Fragment and precursor tolerances of 20 ppm and 0.6 Da were specifie […]

Citations

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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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