Version 3 (modified by b.hoekman@…, 3 years ago)

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Module Settings

Module Properties

Author: openMS
Instrument: Orbitrap
Data processing step: Feature Quantitation
Program: OpenMS Feature Quantitation (centroid)
Version: 1.7

Description

Settings for the centroid mode feature quantification based on the suggested settings on the website of openMS!

Settings

<?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="FeatureFinder" description="Detects two-dimensional features in LC-MS data.">
    <ITEM name="version" value="1.7.0" type="string" description="Version of the tool that generated this parameters file." tags="advanced" />
    <NODE name="1" description="Instance &apos;1&apos; section for &apos;FeatureFinder&apos;">
      <ITEM name="in" value="" type="string" description="input file (valid formats: &apos;mzML&apos;)" tags="input file" />
      <ITEM name="out" value="" type="string" description="output file (valid formats: &apos;featureXML&apos;)" tags="output file" />
      <ITEM name="seeds" value="" type="string" description="User-specified seed list. This feature is not supported by all algorithms! (valid formats: &apos;featureXML&apos;)" tags="input file" />
      <ITEM name="type" value="centroided" type="string" description="FeatureFinder algorithm type" restrictions="centroided,isotope_wavelet,mrm" />
      <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 software testing only)" tags="advanced" restrictions="true,false" />
      <NODE name="algorithm" description="Algorithm section">
        <ITEM name="debug" value="false" type="string" description="When debug mode is activated, several files with intermediate results are written to the folder &apos;debug&apos; (do not use in parallel mode)." restrictions="true,false" />
        <NODE name="intensity" description="Settings for the calculation of a score indicating if a peak&apos;s intensity is significant in the local environment (between 0 and 1)">
          <ITEM name="bins" value="10" type="int" description="Number of bins per dimension (RT and m/z). The higher this value, the more local the intensity significance score is.#br#This parameter should be decreased, if the algorithm is used on small regions of a map." restrictions="1:" />
        </NODE>
        <NODE name="mass_trace" description="Settings for the calculation of a score indicating if a peak is part of a mass trace (between 0 and 1).">
          <ITEM name="mz_tolerance" value="0.004" type="float" description="Tolerated m/z deviation of peaks belonging to the same mass trace.#br#It should be larger than the m/z resolution of the instument.#br#This value must be smaller than that 1/charge_high!" restrictions="0:" />
          <ITEM name="min_spectra" value="10" type="int" description="Number of spectra that have to show a similar peak mass in a mass trace." restrictions="1:" />
          <ITEM name="max_missing" value="1" type="int" description="Number of spectra where a high mass deviation or missing peak is acceptable.#br#This parameter should be well below &apos;min_spectra&apos;!" restrictions="0:" />
          <ITEM name="slope_bound" value="0.1" type="float" description="The maximum slope of mass trace intensities when extending from the highest peak.#br#This parameter is important to seperate overlapping elution peaks.#br#It should be increased if feature elution profiles fluctuate a lot." restrictions="0:" />
        </NODE>
        <NODE name="isotopic_pattern" description="Settings for the calculation of a score indicating if a peak is part of a isotoipic pattern (between 0 and 1).">
          <ITEM name="charge_low" value="1" type="int" description="Lowest charge to search for." restrictions="1:" />
          <ITEM name="charge_high" value="4" type="int" description="Highest charge to search for." restrictions="1:" />
          <ITEM name="mz_tolerance" value="0.005" type="float" description="Tolerated m/z deviation from the theoretical isotopic pattern.#br#It should be larger than the m/z resolution of the instument.#br#This value must be smaller than that 1/charge_high!" restrictions="0:" />
          <ITEM name="intensity_percentage" value="10" type="float" description="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present." tags="advanced" restrictions="0:100" />
          <ITEM name="intensity_percentage_optional" value="0.1" type="float" description="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing." tags="advanced" restrictions="0:100" />
          <ITEM name="optional_fit_improvement" value="2" type="float" description="Minimal percental improvement of isotope fit to allow leaving out an optional peak." tags="advanced" restrictions="0:100" />
          <ITEM name="mass_window_width" value="25" type="float" description="Window width in Dalton for precalcuation of estimated isotope distribtions." tags="advanced" restrictions="1:200" />
        </NODE>
        <NODE name="seed" description="Settings that determine which peaks are considered a seed">
          <ITEM name="min_score" value="0.8" type="float" description="Minimum seed score a peak has to reach to be used as seed.#br#The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score.#br#If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score." restrictions="0:1" />
        </NODE>
        <NODE name="fit" description="Settings for the model fitting">
          <ITEM name="epsilon_abs" value="0.0001" type="float" description="Absolute epsilon used for convergence of the fit." tags="advanced" restrictions="0:" />
          <ITEM name="epsilon_rel" value="0.0001" type="float" description="Relative epsilon used for convergence of the fit." tags="advanced" restrictions="0:" />
          <ITEM name="max_iterations" value="500" type="int" description="Maximum number of iterations of the fit." tags="advanced" restrictions="1:" />
        </NODE>
        <NODE name="feature" description="Settings for the features (intensity, quality assessment, ...)">
          <ITEM name="min_score" value="0.7" type="float" description="Feature score threshold for a feature to be reported.#br#The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks." restrictions="0:1" />
          <ITEM name="min_isotope_fit" value="0.8" type="float" description="Minimum isotope fit of the feature before model fitting." tags="advanced" restrictions="0:1" />
          <ITEM name="min_trace_score" value="0.5" type="float" description="Trace score threshold.#br#Traces below this threshold are removed after the model fitting.#br#This parameter is important for features that overlap in m/z dimension." tags="advanced" restrictions="0:1" />
          <ITEM name="min_rt_span" value="0.333" type="float" description="Minimum RT span in relation to extended area that has to remain after model fitting." tags="advanced" restrictions="0:1" />
          <ITEM name="max_rt_span" value="2.5" type="float" description="Maximum RT span in relation to extended area that the model is allowed to have." tags="advanced" restrictions="0.5:" />
          <ITEM name="rt_shape" value="symmetric" type="string" description="Choose model used for RT profile fitting. If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used." tags="advanced" restrictions="symmetric,asymmetric" />
          <ITEM name="max_intersection" value="0.35" type="float" description="Maximum allowed intersection of features." tags="advanced" restrictions="0:1" />
          <ITEM name="reported_mz" value="monoisotopic" type="string" description="The mass type that is reported for features.#br#&apos;maximum&apos; returns the m/z value of the highest mass trace.#br#&apos;average&apos; returns the intensity-weighted average m/z value of all contained peaks.#br#&apos;monoisotopic&apos; returns the monoisotopic m/z value derived from the fitted isotope model." restrictions="maximum,average,monoisotopic" />
        </NODE>
        <NODE name="user-seed" description="Settings for user-specified seeds.">
          <ITEM name="rt_tolerance" value="5" type="float" description="Allowed RT deviation of seeds from the user-specified seed position." restrictions="0:" />
          <ITEM name="mz_tolerance" value="1.1" type="float" description="Allowed m/z deviation of seeds from the user-specified seed position." restrictions="0:" />
          <ITEM name="min_score" value="0.5" type="float" description="Overwrites &apos;seed:min_score&apos; for user-specified seeds. The cutoff is typically a bit lower in this case." restrictions="0:1" />
        </NODE>
        <NODE name="debug" description="">
          <ITEM name="pseudo_rt_shift" value="500" type="float" description="Pseudo RT shift used when ." tags="advanced" restrictions="1:" />
        </NODE>
      </NODE>
    </NODE>
  </NODE>
</PARAMETERS>