This is an old revision of the document!
IRMa stands for Interprétation des Résultats Mascot® (Mascot® Results Interpretation).
Download is available at the following FTP site : ftp://ftp.cea.fr/pub/edyp/irma
References :
Veronique Dupierris; Christophe Masselon; Magali Court; Sylvie Kieffer-Jaquinod; Christophe Bruley
A toolbox for Validation of mass spectrometry peptides identification and Generation of database: IRMa
Bioinformatics 2009; doi: 10.1093/bioinformatics/btp301
IRMa toolbox provides an interactive application to assist in the validation of Mascot® search results. IRMa reads MASCOT® result (using Matrix Science® Parser distributed free of charge) and automatically filters identified peptides. All relevant information is displayed in a structured manner, showing “proteins hits” details. User can then manually or automatically confirm or reject individual peptide spectrum matches.
Screenshots available here.
Under Construction
Find quick answer to your questions in the How to section.
Filtering
Automatique filtering : few filters can be applied at any stage of the validation purpose. These filters can be based on the PSM score and rank, on PTM or regular expressions on PSM properties. The filters classifies the PSM into significative group (used for the protien identification) or ambiguous group (unrelevant for identification). Manual filtering : User can choose to manually set a ambiguous PSM as significative and inversly Dynamic grouping during validation
Export
export to Excel® Generate PDF document with annotated spectra and matched fragment ions table for publication purposes. Create Identification Results Databases
Automatic and Batch mode
Batch mode to automatically validate multiple identification results Automatic mode integrated to Mascot Daemon
IRMa can be used in three different ways :
But what ever mode you use, the IRMa principles is the entry point to understand this toolbox.
Validated identification results can be exported within a relational database. These database must implements the Mass Spectrometry Identification database models.
Legend :
release date : IRMa version number (DB model version compatibility)
24/01/2012 : IRMa 1.30.2 (D.3 & D.4 & E.1)
20/12/2011 : IRMa 1.30.1 (D.3 & D.4 & E.1)
19/12/2011 : IRMa 1.30.0 (D.3 & D.4 & E.1)
28/10/2011 : IRMa 1.29.2 (D.3 & D.4 & E.1)
03/08/2011 : IRMa 1.29.1 (D.3 & D.4 & E.1)
28/07/2011 : IRMa 1.29.0 (D.3 & D.4 & E.1)
01/02/2011 : IRMa 1.28.1 (D.3 & D.4 & E.1)
20/10/2010 : IRMa 1.28.0 (D.3 & D.4 & E.1)
19/10/2010 : IRMa 1.27.3 (D.3 & D.4)
11/10/2010 : IRMa 1.27.2 (D.3 & D.4)
30/07/2010 : IRMa 1.27.1 (D.3 & D.4)
24/09/2010 : IRMa 1.27.0 (D.3 & D.4)
27/07/2010 : IRMa 1.26.1 (D.3)
20/07/2010 : IRMa 1.26.0 (D.3)
25/06/2010 : IRMa 1.25.0 (D.3)
10/05/2010 : IRMa 1.24.2 (D.3)
06/05/2010 : IRMa 1.24.1 (D.3)
15/04/2010 : IRMa 1.24.0 (D.3)
01/12/2009 : IRMa 1.23.2 (D.2)
13/01/2010 : IRMa 1.23.1 (D.2)
01/12/2009 : IRMa 1.23.0 (D.2)
18/09/2009 : IRMa 1.22.2 (D.2)
28/04/2009 : IRMa 1.22.0 (D.2)
05/03/2009 : IRMa 1.21.0 (D.1)
09/10/2008 : IRMa 1.20.1