IRMa userguide

userguide:definitions

Anonymous (anonymous@undisclosed.example.com) — 2009-12-01T11:14:03+0200

Definitions Hit (ou protein hit) A hit is a collection of proteins identified by a set of peptides or peptide-sequence matches. Mascot assigns up to ten peptide sequences of each submitted spectra. Each peptide sequences belongs to one or more proteins. Proteins that span the same set of peptides, or a subset, are collapsed into a single hit.

userguide:export_db

Anonymous (anonymous@undisclosed.example.com) — 2016-07-25T10:54:02+0200

Database Export Many validated identification results can be exported within a relational database. This feature requires * Postgresql * an existing database For more information on MSI db, see corresponding page Connecting to a database * Disconnect from the database and quit pgAdmin III

userguide:feature

Anonymous (anonymous@undisclosed.example.com) — 2009-12-01T10:59:57+0200

Main Features Automatic Filtering Since a Mascot dat file is open, IRMa allows you to apply filter rules. This rules assigns peptide-sequence matches (PSM) to significant or ambiguous categories according to different criteria such as score, rank or mandatory post-translational modifications.

userguide:filtres

Anonymous (anonymous@undisclosed.example.com) — 2011-12-19T16:32:55+0200

Parse and filtering When opening a Mascot identification file (dat file), user should specifiy parameters for Mascot parse. Indeed, the first mandatory step is to parse the dat file using free of charge parser distributed by Matrix Science. Mascot Parse

userguide:fragmentationcontent

Anonymous (anonymous@undisclosed.example.com) — 2011-04-12T11:55:57+0200

Petide Fragmentation MS/MS Fragmentation of AHVSFKPTVAQQR, Fixed modifications: Carbamidomethyl (C) (apply to specified residues or termini only) 72.044390035 209.10330203499998 308.17171603500003 395.203744035 542.272158035 670.367121035 767.41988…

userguide:fragmentmatchescontent

Anonymous (anonymous@undisclosed.example.com) — 2011-04-12T11:52:27+0200

Fragment matches example MS/MS fragments matches of AHVSFKPTVAQQR, Fixed modifications: Carbamidomethyl (C) (apply to specified residues or termini only). This corresponding mascot result for this peptide is shown below. Here is the corresponding xml serialization of the fragmentation matches.

userguide:ihm

Anonymous (anonymous@undisclosed.example.com) — 2009-12-01T15:17:50+0200

Graphical User Interface IRMa main window is splitted in three panels : the left one allow users to browse protein hits, the rigth one shows submitted queries and peptide sequences matching this queries. The center panel contains tabs representing Protein hit details, Search parameters, Query details and the list of identified proteins.

userguide:msidbmodeld.3-desc

Anonymous (anonymous@undisclosed.example.com) — 2010-07-08T09:22:44+0200

MSIdb version D.3 List of tables * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *

userguide:msidbmodeld.4-desc

Anonymous (anonymous@undisclosed.example.com) — 2011-04-12T11:45:23+0200

Model D.4 List of tables * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * admin_infos (Physical Name: admin_infos)

userguide:msimodel18

Anonymous (anonymous@undisclosed.example.com) — 2009-02-03T13:36:06+0200

MSI model version 18

userguide:quantification

Anonymous (anonymous@undisclosed.example.com) — 2010-09-24T17:35:49+0200

Quantification :!: This page is under construction Problèmes avec la vue centrée sur les ratios de Distiller Dans les cas de quantification avec précurseur pré-traitées par Mascot Distiller il existent un certains nombre de problèmes liés aux ratios.