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 IRMa batch documentation.

An exemple is done in the runautoIRMa.bat file under <IRMa_HOME>

To run the autoIRMa on a Mascot® identification result :

java -Djava.library.path=./lib -Xms256m -Xmx512m -cp IRMa-<version>.jar cea.irma.autoIRMa <resultURL> <mascotDatPath> -s <scriptFile>

Where

• <resultFile> is the mascot result file (e.g /20080521/F035548.dat)
• <mascotDatPath> is the path to directories containing mascot dat files
• <scriptFile> specify the xml file containing irma instructions. (See IRMa batch documentation)

The main purpose of this mode is that it permits IRMa integration into existing, automatic, workflows such as Mascot Daemon®.

IRMa comes with three Visual Basic scripts (<IRMa_HOME>/VBscripts) to allow to run autoIRMa using wscript so from Mascot Daemon® :

• autoIRMa.vbs : Runs autoIRMa on a Mascot® search result. Parameters resultfile (specifying with .dat file to validate) and script (specifying which script file to use) are mandatory.

This VBScript defines a variable indicating the <IRMa_HOME> directory and an other variable indicating where Mascot® .dat files are stored. This latest directory should be accessible from the Mascot Daemon® Service Owner.
-Xms argument should NOT be specified in the VBScript !!

• renameMGF.vbs : Rename MGF generated by the task if it import data from raw files using MascotDistiller®. Parameter peakfile is mandatory

• master.vbs : Runs autoIRMa.vbs and renameMGF.vbs. If the task is run using MGF files the renameMGF is not necessary but the script still works. Parameters are those mandatory in both sub VBScripts.

IRMa can be invoked, as an external process, by the Mascot Daemon® software, which controls raw data pre-processing and Mascot® searches. When defining a new Mascot Daemon® task, you can invoke a script provided in IRMa distribution.

1. Select “External Process in Actions group
2. Enter the following command in the After each search section, in order to be able to validate each Mascot® search result.

  wscript "[Path\To\IRMaVBScripts]\master.vbs" /peakfile:"<cachedpeaklist>" 
     /resultfile:"<resultfilename>" 
     /script:"[Path\To\IRMaScripts]\script_TEST_DB.xml"

• [Path\To\IRMaVBScripts] : to be replaced by the absolute path to directory where VBScript are stored. It is RECOMMENDED to create a directory for each version of IRMa in order to be sure to use appropriated scripts.
• [Path\To\IRMaScripts] : to be replaced by the absolute path to directory where IRMa instruction scripts are stored.
• <cachedpeaklist> and <resultfilename> are automatically replaced by, respectively, the full path to generated MGF (if a Data Import Filter has been specified in task) and the Mascot Result file.

  <delete.Proteins>
    <parameters>
      <parameter name="is.freeze.fp.analysis">
        <value class="boolean">true</value>
      </parameter>
      <parameter name="peptides.count">
        <value class="int">1</value>
      </parameter>
      <parameter name="peptides.score">
        <value class="int">20</value>
      </parameter>
      <parameter name="peptides.unicity">
        <value class="boolean">true</value>
      </parameter>
    </parameters>
  </delete.Proteins>

Nota : The “filter.master.rule.operation” parameter can be :

• CONTAINS_RULE
• NOT_CONTAINS_RULE
• BEGINS_WITH_RULE
• ENDS_WITH_RULE

<filter.Master>
    <parameters>
      <parameter name="filter.master.rule.map"> <!-- FIRST Parameter : A collection of rule -->
        <value class="map">
          <entry>
            <string>R1</string>
            <cea.irma.model.validation.MasterProteinFilterRule>
              <properties>
                <entry>
                  <string>filter.master.rule.name</string>
                  <parameter name="filter.master.rule.name">
                    <value class="string">R1</value>
                  </parameter>
                </entry>
                <entry>
                  <string>filter.master.rule.operation</string>
                  <parameter name="filter.master.rule.operation">
                    <value class="cea.irma.model.validation.MasterProteinFilterRule$RuleOperation">CONTAINS_RULE</value>
                  </parameter>
                </entry>
                <entry>
                  <string>filter.master.applies.accession</string>
                  <parameter name="filter.master.applies.accession">
                    <value class="boolean">true</value>
                  </parameter>
                </entry>
                <entry>
                  <string>filter.master.applies.description</string>
                  <parameter name="filter.master.applies.description">
                    <value class="boolean">false</value>
                  </parameter>
                </entry>
                <entry>
                  <string>filter.master.searched.string</string>
                  <parameter name="filter.master.searched.string">
                    <value class="string">_HUMAN</value>
                  </parameter>
                </entry>
              </properties>
            </cea.irma.model.validation.MasterProteinFilterRule>
          </entry>
        </value>
      </parameter> <!-- END of FIRST Parameter -->
      <parameter name="filter.master.rules.composition"> <!-- SECOND Parameter : The composition of rules previously set -->
        <value class="string">R1</value>
      </parameter>
    </parameters> <!-- END of SECOND Parameter -->
  </filter.Master>