A toolbox for validation of mass spectrometry peptides identification and generation of database: IRMa.
CONCLUSIONS
The IRMa toolbox provides an interactive application to assist in the validation of Mascot search results. It allows automatic filtering of Mascot identification results as well as manual confirmation or rejection of individual PSM (a match between a fragmentation mass spectrum and a peptide). Dynamic grouping and coherence of information are maintained by the software in real time. Validated results can be exported under various forms, including an identification database (MSIdb). This allows biologists to compile search results from a whole study in a unique repository in order to provide a summarized view of their project. IRMa also features a fully automated version that can be used in a high-throughput pipeline. Given filter parameters, it can delete hits with no significant PSM, regroup hits identified by the same peptide(s) and export the result to the specified format without user intervention.


BACKGROUND
http://biodev.extra.cea.fr/docs/irma (java 1.5 or higher needed).
Fondation Rhône-Alpes Futur, 69003 Lyon, France.
Véronique
V
Dupierris
Christophe
C
Masselon
Magali
M
Court
Sylvie
S
Kieffer-Jaquinod
Christophe
C
Bruley
D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D013058:Mass Spectrometry / Q000379:methods; D010455:Peptides / Q000032:analysis / Q000737:chemistry*; D040901:Proteomics / Q000379:methods; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein / Q000379:methods; D012984:Software
D010455:Peptides