wiki:openMS_featureQuant_IonTrap_bhoekman_v1

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

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Module Settings

Module Properties

Author: bhoekman
Instrument: IonTrap
Data processing step: Feature Quantitation
Program: OpenMS Feature Quantitation
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.

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>