| OpenMS 2.5.0

FeatureFinderMRM

The feature detection application for quantitation.

pot. predecessor tools | FeatureFinderMRM | pot. successor tools
| FeatureLinkerUnlabeled (or another feature grouping tool)
MapAlignerPoseClustering (or another alignment tool)

This module identifies "features" in a LC/MS map. By feature, we understand a peptide in a MS sample that reveals a characteristic isotope distribution. The algorithm computes positions in rt and m/z dimension and a charge estimate of each peptide.

How to find suitable parameters and details of the different algorithms implemented are described in the TOPP tutorial.

Specialized tools are available for some experimental techniques: IsobaricAnalyzer.

The command line parameters of this tool are:

    FeatureFinderMRM -- Detects two-dimensional features in LC-MS data.

    Full documentation: http://www.openms.de/documentation/TOPP_FeatureFinderMRM.html

    Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

    To cite OpenMS:

      Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.

    Usage:

      FeatureFinderMRM <options>

    This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript

    ion or use the --helphelp option.

    Options (mandatory options marked with '*'):

      -in <file>*        Input file (valid formats: 'mzML')

      -out <file>*       Output file (valid formats: 'featureXML')

    Common TOPP options:

      -ini <file>        Use the given TOPP INI file

      -threads <n>       Sets the number of threads allowed to be used by the TOPP tool (default: '1')

      -write_ini <file>  Writes the default configuration file

      --help             Shows options

      --helphelp         Shows all options (including advanced)

    The following configuration subsections are valid:

     - algorithm   Algorithm section

    You can write an example INI file using the '-write_ini' option.

    Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.

    For more information, please consult the online documentation for this tool:

      - http://www.openms.de/documentation/TOPP_FeatureFinderMRM.html

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+FeatureFinderMRM Detects two-dimensional features in LC-MS data.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'FeatureFinderMRM'
in input file input file*.mzML
out output file output file*.featureXML
log Name of log file (created only when specified)
debug 0 Sets the debug level
threads 1 Sets the number of threads allowed to be used by the TOPP tool
no_progress false Disables progress logging to command line true,false
force false Overwrite tool specific checks.true,false
test false Enables the test mode (needed for internal use only)true,false
+++algorithm Algorithm section
min_rt_distance 10.0 Minimal distance of MRM features in seconds.0.0:∞
min_num_peaks_per_feature 5 Minimal number of peaks which are needed for a single feature 1:∞
min_signal_to_noise_ratio 2.0 Minimal S/N ratio a peak must have to be taken into account. Set to zero if the MRM-traces contains mostly signals, and no noise.0.0:∞
write_debug_files false If set to true, for each feature a plot will be created, in the subdirectory 'debug'true,false
resample_traces false If set to true, each trace, which is in this case a part of the MRM monitoring trace with signal is resampled, using the minimal distance of two data points in RT dimension true,false
write_debuginfo false If set to true, debug messages are written, the output can be somewhat lengthy.true,false

For the parameters of the algorithm section see the algorithms documentation:
OpenMS::FeatureFinderAlgorithmMRM FeatureFinderAlgorithmMRM