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IRMa Toolbox

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

What is IRMa

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.

Features

  • Easy navigation within identification result
  • Automatic or Manual filtering
  • Dynamic grouping during validation
  • Export validated results to Excel®
  • Generate PDF document with annotated spectra and matched fragment ions table for publication purposes.
  • Export validated results in a relational database
  • Batch mode to automatically validate multiple identification results
  • Automatic mode integrated to Mascot Daemon

Documentations

:!: Under Construction

Getting Started

How To

Find quick answer to your questions in the How to section.

Concepts

The concepts page will give you information on concepts used by this toolbox.


to migrate on other pages

IRMa can be used in three different ways :

  • Graphical : IRMa provides a graphical user interface allowing users to validate Mascot results manually or by applying filters and to navigate within the identification result.
  • Batch : users can create scripts in order to repeat IRMa commands (parse, filter, save, export, etc) among many Mascot files.
  • AutoIRMa : IRMa can also be run from command line. This feature allows you to integrate IRMa with Mascot daemon utility in order to create a fully automated pipeline.
  • Scripts : Some hints on how to use scripts for Batch and AutoIRMa

Export to Relational Database

Validated identification results can be exported within a relational database. These database must implements the Mass Spectrometry Identification database models.

Versions

Which hEIDI/IRMa/MSIdb Legend :

release date : IRMa version number (DB model version compatibility)

05/10/2012 : IRMa 1.31.0 (D.3 & D.4 & E.2) 12/03/2012 : IRMa 1.30.4 (D.3 & D.4 & E.2) :!: Not E.1. any more, execute migration E.1 to E.2
02/03/2012 : IRMa 1.30.3 (D.3 & D.4 & E.1)
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

Release Note

start.txt · Dernière modification: 2012/10/05 07:56 par 132.168.72.131