MSMSpdbb specifications

Information


Unique identifier OMICS_24076
Name MSMSpdbb
Alternative name Multi-Strain Mass Spectrometry prokaryote database builder
Software type Application/Script
Interface Command line interface
Restrictions to use None
Output format FASTA
Operating system Unix/Linux, Windows
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Requirements
Blast, wget
Maintained No

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Publication for Multi-Strain Mass Spectrometry prokaryote database builder

MSMSpdbb citations

 (2)
library_books

Large scale analysis of amino acid substitutions in bacterial proteomics

2016
BMC Bioinformatics
PMCID: 5100282
PMID: 27821049
DOI: 10.1186/s12859-016-1301-5

[…] translational modifications (PTM)[].To overcome these problems, some algorithms use a set of all possible modified peptides. One of the solution for SAPs identification is an approach demonstrated in MSMSpdbb [], a protein database which comprises all known peptide variants. The database is constructed from all known homologous peptide sequences for a given species merged into synthetic sequences. […]

library_books

Proteogenomic Analysis of Polymorphisms and Gene Annotation Divergences in Prokaryotes using a Clustered Mass Spectrometry Friendly Database*

2010
PMCID: 3013451
PMID: 21030493
DOI: 10.1074/mcp.M110.002527

[…] The sequence clustering provided by MSMSpdbb also allows the reporting of annotated genes that are specific to one or some of the genomes, thereby reducing annotation error discrepancies. For example, the annotated protein MT2297 [A3] i […]

MSMSpdbb institution(s)
The Gade Institute, Section for Microbiology and Immunology, University of Bergen, Bergen, Norway; Proteomic Unit of Bergen, Department of Biomedicine, University of Bergen, Bergen, Norway; Department of Microbiology and Immunology, Haukeland University Hospital, Bergen, Norway
MSMSpdbb funding source(s)
Supported by the Norwegian Research Council (175141) (FUGE).

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