====== IRMa Principles ======

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===== Concepts =====

  * Data concepts 
    * [[prot_peptides|Proteins, Proteins Group and Peptides]]
    * IRMa project 
  * Operations definitions
    * [[Parse|parse]] dat file
    * [[Filtering|Filtering]]
    * [[export|Exporting to]] MSIdb
    * [[export_result|Exporting to]] XLS

 

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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