IRMa

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.

This automatic classification can always be adjusted; the user can restore PSMs from the ambiguous group to the significant group or vice versa.

The identification result can then be browsed and the same information and grouping shown in the Mascot result page are available but displayed in a structured and accessible layout by IRMa. Fragmentation spectra and matching ions can also be visualised in order to accept or reject manually incorrect matches.

IRMa provides online access to public datasources for each identified protein, depending on the databank used by Mascot. The later version of IRMa allow users to customise the URL template that will be used for his own databanks.

IRMa provides some statistics about spectra or PSM :

• For “decoy” searches, the false positive rate is calculated according to PSM classified as significant.
• The number of assigned spectra is also available
• error mass distribution for all identified spetra is calculated providing valuable information on

IRMa will ensure that the exact same sequence cannot appear twice in the significant category. Dynamic classification has an impact on protein hits: when a PSM is declared ambiguous, it becomes irrelevant to proteins identification. IRMa takes into account these changes to ensure consistency of information such as protein coverage and identification score and dynamically proposes new protein hit sets and sub-sets based on significant PSMs. For instance, two proteins of a same hit that initially shared only a sub-set of PSMs can become indistinguishable (all significant PSMs are shared) if specific PSMs are judged ambiguous.

IRMa allow users to export their results (or parts of it) in many different formats :

• Identified protein's sequences can be exported in fasta format for further analysis (blast for instance)
• The whole identification result can be exported in Microsoft Excel format. Users can customise the content of this export.
• Identification's details can be exported to a PDF format including graphical representation of annotated spectra.
• Identification results can be exported to relational databases. By doing this, users can then compile many identifications within a unique database. See schéma
• Spectra assigned or not can be exported in PKL or MGF format.