====== IRMa Toolbox ======

IRMa stands for **I**nterprétation des **R**ésultats **Ma**scot® (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: [[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp301|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 [[screenshots|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_to_relational_database|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 ====

  * The [[instalGuide|installation guide]] gives informations on the distribution content.
  * Read our [[firstSteps|quick start guide]].


==== How To  ====

Find quick answer to your questions in the [[how_to|How to]] section.

==== Concepts  ====

The [[principle|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 : 
  * [[userGuide|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.
  * [[batchUserGuide|Batch]] : users can create scripts in order to repeat IRMa commands (parse, filter, save, export, etc) among many Mascot files. 
  * [[autoUserGuide|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.
  * [[autoUserGuide#scripts|Scripts]] : Some hints on how to use scripts for Batch and AutoIRMa


==== Export to Relational Database ====
Validated identification results can be [[userGuide:export_db|exported]] within a relational database. These database must implements the [[MSIdb|Mass Spectrometry Identification database models]].

==== Versions ====

{{:msidb_irma_heidi_compat.png |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 \\

[[ReleaseNote|Release Note]]