wiki:openMS_featureQuant_IonTrap_bhoekman_v1

Version 9 (modified by b.hoekman@…, 7 years ago) (diff)

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Module Settings

Module Properties

Author: bhoekman
Instrument: IonTrap
Data processing step: Feature Quantitation
Program: OpenMS Feature Quantitation (simplest)
Version: 1.2

Description

Settings as used for the parsing of IonTrap LC-MS chromatograms. pls. note that these setting are for a quite old version of OpenMS it is advisable to upgrade them for newer versions of OpenMS. (Never version of OpenMS have removed the feature detection method used in this settings file, use this file if possible with version 1.2 of OpenMS)

Settings

<?xml version="1.0" encoding="ISO-8859-1"?>
<PARAMETERS version="1.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <NODE name="FeatureFinder" description="">
    <NODE name="1" description="Instance '1' section for 'FeatureFinder'">
      <ITEM name="in" value="" type="string" description="input file (valid formats: 'mzData')" advanced="false" />
      <ITEM name="out" value="" type="string" description="output feature list (valid formats: 'featureXML')" advanced="false" />
      <ITEM name="type" value="simplest" type="string" description="FeatureFinder algorithm type#br#" advanced="false" restrictions="isotope_wavelet,isotope_wavelet_nofit,picked_peak,simple,simplest" />
      <ITEM name="log" value="TOPP.log" type="string" description="Location of the log file" advanced="false" />
      <ITEM name="debug" value="0" type="int" description="Sets the debug level" advanced="false" />
      <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" advanced="false" restrictions="true,false" />
      <NODE name="algorithm" description="Algorithm section">
        <NODE name="seeder" description="Settings for the seeder (Determines potential feature regions)">
          <ITEM name="min_intensity" value="0" type="float" description="Absolute value for the minimum intensity of a seed. If set to 0, a fixed percentage of the intensity of the largest peak is taken (see intensity_perc)." advanced="false" restrictions="0-" />
          <ITEM name="signal_to_noise" value="10" type="float" description="SignalToNoise (S/N) ratio." advanced="false" restrictions="0-" />
        </NODE>
        <NODE name="extender" description="Settings for the extender (Collects all peaks belonging to a feature)">
          <ITEM name="dist_mz_up" value="6" type="float" description="Maximum high m/z distance of peak in the region/boundary from the seed." advanced="false" restrictions="0-" />
          <ITEM name="dist_mz_down" value="2" type="float" description="Maximum low m/z distance of peak in the region/boundary from the seed." advanced="false" restrictions="0-" />
          <ITEM name="dist_rt_up" value="30" type="float" description="Maximum high RT distance of peak in the region/boundary from the seed." advanced="false" restrictions="0-" />
          <ITEM name="dist_rt_down" value="30" type="float" description="Maximum low RT distance of peak in the region/boundary from the seed." advanced="false" restrictions="0-" />
          <ITEM name="priority_thr" value="-0.1" type="float" description="Minimum priority for data points to be included into the boundary of the feature (default 0.0). The priority of a data point is a function of its intensity and its distance to the last point included into the feature region. Setting this threshold to zero or a very small value is usually a good idea." advanced="true" />
          <ITEM name="intensity_factor" value="0.03" type="float" description="Influences for intensity (ion count) threshold in the feature extension. We include only raw data points into this region if their intensity is larger than [intensity_factor * (intensity of the seed)]." advanced="false" restrictions="0-1" />
        </NODE>
        <NODE name="fitter" description="Settings for the modefitter (Fits a model to the data determinging the probapility that they represent a feature.)">
          <ITEM name="fit_algorithm" value="simple" type="string" description="Fitting algorithm type (internal parameter)." advanced="true" restrictions="simple,simplest,wavelet" />
          <ITEM name="max_iteration" value="500" type="int" description="Maximum number of iterations for fitting with Levenberg-Marquardt algorithm." advanced="true" restrictions="1-" />
          <ITEM name="deltaAbsError" value="0.0001" type="float" description="Absolute error used by the Levenberg-Marquardt algorithm." advanced="true" restrictions="0-" />
          <ITEM name="deltaRelError" value="0.0001" type="float" description="Relative error used by the Levenberg-Marquardt algorithm." advanced="true" restrictions="0-" />
          <ITEM name="tolerance_stdev_bounding_box" value="3" type="float" description="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data" advanced="true" restrictions="0-" />
          <ITEM name="intensity_cutoff_factor" value="0.05" type="float" description="Cutoff peaks with a predicted intensity below intensity_cutoff_factor times the maximal intensity of the model" advanced="false" restrictions="0-1" />
          <ITEM name="feature_intensity_sum" value="1" type="int" description="Determines what is reported as feature intensity.#br#1: the sum of peak intensities;#br#0: the maximum intensity of all peaks" advanced="true" restrictions="0-1" />
          <NODE name="min_num_peaks" description="Required number of peaks for a feature.">
            <ITEM name="final" value="5" type="int" description="Minimum number of peaks left after cutoff. If smaller, feature will be discarded." advanced="false" restrictions="1-" />
            <ITEM name="extended" value="10" type="int" description="Minimum number of peaks after extension. If smaller, feature will be discarded." advanced="false" restrictions="1-" />
          </NODE>
          <NODE name="rt" description="Model settings in RT dimension.">
            <ITEM name="interpolation_step" value="1" type="float" description="Step size in seconds used to interpolate model for RT." advanced="false" restrictions="0-" />
          </NODE>
          <NODE name="mz" description="Model settings in m/z dimension.">
            <ITEM name="interpolation_step" value="0.03" type="float" description="Interpolation step size for m/z." advanced="false" restrictions="0.001-" />
            <NODE name="model_type" description="">
              <ITEM name="first" value="1" type="int" description="Numeric id of first m/z model fitted (usually indicating the charge state), 0 = no isotope pattern (fit a single gaussian)." advanced="false" restrictions="0-" />
              <ITEM name="last" value="4" type="int" description="Numeric id of last m/z model fitted (usually indicating the charge state), 0 = no isotope pattern (fit a single gaussian)." advanced="false" restrictions="0-" />
            </NODE>
          </NODE>
          <NODE name="quality" description="Fitting quality settings.">
            <ITEM name="type" value="Correlation" type="string" description="Type of the quality measure used to assess the fit of model vs data." advanced="true" restrictions="Correlation,RankCorrelation" />
            <ITEM name="minimum" value="0.25" type="float" description="Minimum quality of fit, features below this threshold are discarded." advanced="false" restrictions="0-1" />
          </NODE>
          <NODE name="isotope_model" description="Settings of the isotope model (m/z).">
            <NODE name="stdev" description="Instrument resolution settings for m/z dimension.">
              <ITEM name="first" value="0.04" type="float" description="First standard deviation to be considered for isotope model." advanced="false" restrictions="0-" />
              <ITEM name="last" value="0.12" type="float" description="Last standard deviation to be considered for isotope model." advanced="false" restrictions="0-" />
              <ITEM name="step" value="0.04" type="float" description="Step size for standard deviations considered for isotope model." advanced="false" restrictions="0-" />
            </NODE>
            <NODE name="averagines" description="Averagines are used to approximate the number of atoms (C,H,N,O,S) which a peptide of a given mass contains.">
              <ITEM name="C" value="0.0443" type="float" description="Number of C atoms per Dalton of the mass." advanced="true" restrictions="0-" />
              <ITEM name="H" value="0.007" type="float" description="Number of H atoms per Dalton of the mass." advanced="true" restrictions="0-" />
              <ITEM name="N" value="0.0012" type="float" description="Number of N atoms per Dalton of the mass." advanced="true" restrictions="0-" />
              <ITEM name="O" value="0.013" type="float" description="Number of O atoms per Dalton of the mass." advanced="true" restrictions="0-" />
              <ITEM name="S" value="0.00037" type="float" description="Number of S atoms per Dalton of the mass." advanced="true" restrictions="0-" />
            </NODE>
            <NODE name="isotope" description="">
              <ITEM name="trim_right_cutoff" value="0.001" type="float" description="Cutoff for averagine distribution, trailing isotopes below this relative intensity are not considered." advanced="true" restrictions="0-" />
              <ITEM name="maximum" value="100" type="int" description="Maximum number of isotopes being used for the IsotopeModel." advanced="true" restrictions="1-" />
              <ITEM name="distance" value="1.000495" type="float" description="Distance between consecutive isotopic peaks." advanced="true" restrictions="0-" />
            </NODE>
          </NODE>
        </NODE>
      </NODE>
    </NODE>
  </NODE>
</PARAMETERS>