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<?xml version="1.0" encoding="ISO-8859-1"?>
<PARAMETERS version="1.3" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_3.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<NODE name="ITRAQAnalyzer" description="Calculates iTRAQ quantitative values for peptides">
<ITEM name="version" value="1.9.0" type="string" description="Version of the tool that generated this parameters file." tags="advanced" />
<NODE name="1" description="Instance '1' section for 'ITRAQAnalyzer'">
<ITEM name="type" value="4plex" type="string" description="iTRAQ experiment type#br#" restrictions="4plex,8plex" />
<ITEM name="in" value="" type="string" description="input raw/picked data file " tags="input file,required" restrictions="*.mzML" />
<ITEM name="out" value="" type="string" description="output consensusXML file with quantitative information" tags="output file,required" restrictions="*.consensusXML" />
<ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" />
<ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" />
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" />
<ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" />
<ITEM name="id_pool" value="" type="string" description="ID pool file to DocumentID's for all generated output files. Disabled by default. (Set to 'main' to use C:/dev/OpenMS/share/OpenMS/IDPool/IDPool.txt)" />
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" />
<NODE name="algorithm" description="Algorithm parameters section">
<NODE name="Extraction" description="">
<ITEM name="select_activation" value="" type="string" description="Operate only on MSn scans where any of its percursors features a certain activation method (usually HCD for iTRAQ). Set to empty string if you want to disable filtering.#br#" restrictions="Collision-induced dissociation,Post-source decay,Plasma desorption,Surface-induced dissociation,Blackbody infrared radiative dissociation,Electron capture dissociation,Infrared multiphoton dissociation,Sustained off-resonance irradiation,High-energy collision-induced dissociation,Low-energy collision-induced dissociation,Photodissociation,Electron transfer dissociation," />
<ITEM name="reporter_mass_shift" value="0.1" type="float" description="Allowed shift (left to right) in Da from the expected position (of e.g. 114.1, 115.1)" restrictions="1e-008:0.5" />
<ITEMLIST name="channel_active" type="string" description="Each channel that was used in the experiment and its description (114-117 for 4plex; 113-121 for 8-plex) in format <channel>:<name>, e.g. "114:myref","115:liver".">
<LISTITEM value="114:l1"/>
<LISTITEM value="115:l2"/>
<LISTITEM value="116:l3"/>
<LISTITEM value="117:lung"/>
</ITEMLIST>
</NODE>
<NODE name="Quantification" description="">
<ITEM name="isotope_correction" value="true" type="string" description="enable isotope correction (highly recommended)" tags="advanced" restrictions="true,false" />
<ITEM name="do_normalization" value="false" type="string" description="Normalize channels? Done by using the Median of Ratios (every channel / Reference). Also the ratio of medians (from any channel and reference) is provided as control measure!" tags="advanced" restrictions="true,false" />
<ITEM name="channel_reference" value="114" type="int" description="number of the reference channel (114-117 for 4plex)" restrictions="113:121" />
<NODE name="isotope_correction" description="Isotope correction matrices for 4plex and 8plex. Only one of them will be used (depending on iTRAQ mode)">
<ITEMLIST name="4plex" type="string" description="override default values (see Documentation); use the following format: <channel>:<-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2' " tags="advanced">
<LISTITEM value="114:0/1/5.9/0.2"/>
<LISTITEM value="115:0/2/5.6/0.1"/>
<LISTITEM value="116:0/3/4.5/0.1"/>
<LISTITEM value="117:0.1/4/3.5/0.1"/>
</ITEMLIST>
<ITEMLIST name="8plex" type="string" description="override default values (see Documentation); use the following format: <channel>:<-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2' " tags="advanced">
<LISTITEM value="113:0/0/6.89/0.22"/>
<LISTITEM value="114:0/0.94/5.9/0.16"/>
<LISTITEM value="115:0/1.88/4.9/0.1"/>
<LISTITEM value="116:0/2.82/3.9/0.07"/>
<LISTITEM value="117:0.06/3.77/2.88/0"/>
<LISTITEM value="118:0.09/4.71/1.88/0"/>
<LISTITEM value="119:0.14/5.66/0.87/0"/>
<LISTITEM value="121:0.27/7.44/0.18/0"/>
</ITEMLIST>
</NODE>
</NODE>
<NODE name="MetaInformation" description="">
<ITEM name="Program" value="OpenMS::ITRAQAnalyzer" type="string" description="" tags="advanced" />
</NODE>
</NODE>
</NODE>
</NODE>
</PARAMETERS>
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