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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="SILACAnalyzer" description="Determination of peak ratios in LC-MS data">
<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 'SILACAnalyzer'">
<ITEM name="in" value="" type="string" description="input file (valid formats: 'mzML')" tags="input file,required" />
<ITEM name="out" value="" type="string" description="output file (valid formats: 'consensusXML')" tags="output file" />
<ITEM name="out_clusters" value="" type="string" description="Optional output file containing data points passing all filters, hence belonging to a SILAC pattern. Points of the same colour correspond to the mono-isotopic peak of the lightest peptide in a pattern. (valid formats: 'consensusXML')" tags="advanced,output file" />
<ITEM name="out_features" value="" type="string" description="Optional output file containing features. (valid formats: 'featureXML')" tags="advanced,output file" />
<ITEM name="out_filters" value="" type="string" description="Additional output file containing all points that passed the filters as txt. Suitable as input for "in_filters" to perform clustering without preceding filtering process. (valid formats: 'consensusXML')" tags="advanced,output file" />
<ITEM name="in_filters" value="" type="string" description="Additional input file containing all points that passed the filters as txt. Use output from "out_filters" to perform clustering only. (valid formats: 'consensusXML')" tags="advanced,output file" />
<ITEM name="out_debug" value="" type="string" description="Filename base for debug output." tags="advanced" />
<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="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" />
<NODE name="algorithm" description="Parameters for the algorithm.">
<ITEM name="allow_missing_peaks" value="false" type="string" description="Low intensity peaks might be missing from the isotopic pattern of some of the peptides. Should such peptides be included in the analysis?" tags="advanced" restrictions="true,false" />
<ITEM name="rt_threshold" value="80" type="float" description="Upper bound for the retention time [s] over which a characteristic peptide elutes. " restrictions="0:" />
<ITEM name="rt_min" value="0" type="float" description="Lower bound for the retention time [s]." restrictions="0:" />
<ITEM name="intensity_cutoff" value="10" type="float" description="Lower bound for the intensity of isotopic peaks in a SILAC pattern." restrictions="0.1:" />
<ITEM name="intensity_correlation" value="0.95" type="float" description="Lower bound for the Pearson correlation coefficient, which measures how well intensity profiles of different isotopic peaks correlate." restrictions="0:1" />
<ITEM name="model_deviation" value="10" type="float" description="Upper bound on the factor by which the ratios of observed isotopic peaks are allowed to differ from the ratios of the theoretic averagine model, i.e. ( theoretic_ratio / model_deviation ) < observed_ratio < ( theoretic_ratio * model_deviation )." restrictions="1:" />
</NODE>
<NODE name="labels" description="Isotopic labels that can be specified in section 'sample'.">
<ITEM name="Arg6" value="6.0201290268" type="float" description="Arg6 mass shift" tags="advanced" restrictions="0:" />
<ITEM name="Arg10" value="10.0082686" type="float" description="Arg10 mass shift" tags="advanced" restrictions="0:" />
<ITEM name="Lys4" value="4.0251069836" type="float" description="Lys4 mass shift" tags="advanced" restrictions="0:" />
<ITEM name="Lys6" value="6.0201290268" type="float" description="Lys6 mass shift" tags="advanced" restrictions="0:" />
<ITEM name="Lys8" value="8.0141988132" type="float" description="Lys8 mass shift" tags="advanced" restrictions="0:" />
<ITEM name="dICPL4" value="4.025107" type="float" description="mass difference between isotope-coded protein labels ICPL 4 and ICPL 0" tags="advanced" restrictions="0:" />
<ITEM name="dICPL6" value="6.020129" type="float" description="mass difference between isotope-coded protein labels ICPL 6 and ICPL 0" tags="advanced" restrictions="0:" />
<ITEM name="dICPL10" value="10.045236" type="float" description="mass difference between isotope-coded protein labels ICPL 10 and ICPL 0" tags="advanced" restrictions="0:" />
<ITEM name="Methyl4" value="4.0202" type="float" description="Methyl4 mass shift" tags="advanced" restrictions="0:" />
<ITEM name="Methyl8" value="8.0202" type="float" description="Methyl8 mass shift" tags="advanced" restrictions="0:" />
<ITEM name="Methyl12" value="12.0202" type="float" description="Methyl12 mass shift" tags="advanced" restrictions="0:" />
<ITEM name="Methyl16" value="16.0202" type="float" description="Methyl16 mass shift" tags="advanced" restrictions="0:" />
<ITEM name="Methyl24" value="24.0202" type="float" description="Methyl24 mass shift" tags="advanced" restrictions="0:" />
<ITEM name="Methyl32" value="32.0202" type="float" description="Methyl32 mass shift" tags="advanced" restrictions="0:" />
</NODE>
<NODE name="sample" description="Parameter describing the sample and its labels.">
<ITEM name="labels" value="[Lys8]" type="string" description="Labels used for labelling the sample. [...] specifies the labels for a single sample. For example, [Lys4,Arg6][Lys8,Arg10] describes a mixtures of three samples. One of them unlabelled, one labelled with Lys4 and Arg6 and a third one with Lys8 and Arg10. For permitted labels see 'advanced parameters', section 'labels'." />
<ITEM name="charge" value="2:2" type="string" description="Range of charge states in the sample, i.e. min charge : max charge." />
<ITEM name="missed_cleavages" value="0" type="int" description="Maximum number of missed cleavages." restrictions="0:" />
<ITEM name="peaks_per_peptide" value="3:3" type="string" description="Range of peaks per peptide in the sample, i.e. min peaks per peptide : max peaks per peptide." tags="advanced" />
</NODE>
</NODE>
</NODE>
</PARAMETERS>
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