IRMa

autouserguide

Anonymous (anonymous@undisclosed.example.com) — 2011-12-19T17:51:43+0200

Automatic Mode Introduction This mode has no user interface. The automatic mode allow to execute a set of operations, defined in a script file, on a specific Mascot® identification result. The script file is the same as the one used in batch mode. See

batchuserguide

Anonymous (anonymous@undisclosed.example.com) — 2010-08-27T14:27:35+0200

Mode Batch Le mode batch permet d'enchainer un ensemble d'opérations de façon automatique, et cela sur un ensemble d'identifications Mascot ou de projets IRMa préalablement sauvegardés. Toutes les opérations sont exécutées sur le premier fichier de données, puis c'est le second qui est entièrement traité

export_result

Anonymous (anonymous@undisclosed.example.com) — 2013-06-03T08:36:21+0200

Export to XLS Once validation have been done, the validated result could be exported to XLS file. * To configure which sheet and which value will be exported, open Tools -> Preference * To export : File --> Export --> Identification Result --> to Excel

features

Anonymous (anonymous@undisclosed.example.com) — 2009-09-11T10:21:48+0200

Features ..... Under Construction .... A list of all features is given here. More detail can be found in standard mode user documentation Navigation 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 identifi…

filtering

Anonymous (anonymous@undisclosed.example.com) — 2012-03-02T16:01:10+0200

Filtering Back to concepts Master Protein Filter By default the protein groups are represented by a master protein. This master protein is the same as the one defined by mascot but it may change once filters and grouping have been applied. If it doesn't suit your needs you have the possibility to change the master proteins one by one in the interface OR, in one step for all the protein groups, by using the associated filter.

firststeps

Anonymous (anonymous@undisclosed.example.com) — 2009-04-16T09:39:56+0200

Back Home Getting Started This tutorial will show you how to validate a Mascot identification result with IRMa. A sample Mascot result file is available in the download section : result_sample.dat. But the same operation could be executed with any Mascot MS/MS Ion Search result.

instalguide

Anonymous (anonymous@undisclosed.example.com) — 2016-07-25T10:49:58+0200

Installation Guide Back Home This page describe the distribution content and how to run each of the 3 availables modes, after briefly presenting them. Requirements * Java version 1.6 or higher must be installed on your computer and the full path to the

msidb

Anonymous (anonymous@undisclosed.example.com) — 2016-08-24T15:11:15+0200

Mass Spectrometry Identification Database What are MSIdb Mass Spectrometry Identification Database or MSI db, are database containing validated identification data. They are populated using IRMa application and then can be exploited using generic database exploration software or the

parse

Anonymous (anonymous@undisclosed.example.com) — 2012-03-02T15:47:18+0200

Parsing Mascot result file Back to concepts To parse a Mascot identification result file (.dat file), user should define some settings. These parameters are the same as the one you can specify in Mascot Search engine. Mascot will use these informations in order to build the report.

principle

Anonymous (anonymous@undisclosed.example.com) — 2012-03-02T16:01:39+0200

IRMa Principles Back Home Concepts * Data concepts * Proteins, Proteins Group and Peptides * IRMa project * Operations definitions * parse dat file * Filtering * Exporting to MSIdb * Exporting to XLS ---------- to migrate on other page 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 s…

prot_peptides

Anonymous (anonymous@undisclosed.example.com) — 2012-03-02T15:28:52+0200

Proteins, groups and peptides Back Concepts When parsing a Mascot identification result the manipulated data are : * queries : a spectra submitted to Mascot for identification * peptide : peptide sequence identified by a query and matching a protein (issued from the searched data bank). Mascot assigns up to ten peptide sequences of each submitted spectra.

releasenote

Anonymous (anonymous@undisclosed.example.com) — 2012-10-05T08:02:41+0200

What's new Back Home IRMa 1.31.0 Feature * Les peptides dupliqués issus d'un même requête n'étaient pas pris en compte dans les grouping (et donc rattachés à aucune protéine). Permet de filter ou non ces peptides lors du parse de .dat (#3987) * Export XLS : Ajout de l'expectation value des peptides (

screenshots

Anonymous (anonymous@undisclosed.example.com) — 2009-03-04T18:24:55+0200

ScreenShots [IRMa main window] [Annotated spectrum view] [Protein hit centric view and Query centric view] [PDF export] [Excel export]

start

Anonymous (anonymous@undisclosed.example.com) — 2012-10-05T07:56:47+0200

IRMa Toolbox IRMa stands for Interprétation des Résultats Mascot® (Mascot® Results Interpretation). Download is available at the following FTP site : 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:

userguide

Anonymous (anonymous@undisclosed.example.com) — 2011-12-19T15:29:31+0200

User Guide Back Home This guide will describe on one hand, the IRMa principles and, one the other hand, how to use the user interface when running the application in standard mode * feature * definitions * ihm * filtres * quantification * export_db