Groups corresponding isotope-labeled features in a feature map.

potential predecessor tools	→ FeatureLinkerLabeled →	potential successor tools
FeatureFinderCentroided (or another feature detection algorithm)		ProteinQuantifier
		TextExporter

This tool provides an algorithm for grouping corresponding features in isotope-labeled experiments. For more details and algorithm-specific parameters (set in the ini file) see "Detailed Description" in the algorithm documentation.

FeatureLinkerLabeled takes one feature map (featureXML file) and stores the corresponding features in a consensus map (consensusXML file). Feature maps can be created from MS experiments (peak data) using one of the FeatureFinder TOPP tools.

See also: FeatureLinkerUnlabeled FeatureLinkerUnlabeledQT

The command line parameters of this tool are:

FeatureLinkerLabeled -- Groups corresponding isotope-labeled features in a feature map.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_FeatureLinkerLabeled.html
Version: 3.3.0-pre-nightly-2024-11-20 Nov 21 2024, 02:34:56, Revision: decb5c8
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

Usage:
  FeatureLinkerLabeled <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: 'featureXML')
  -out <file>*       Output file (valid formats: 'consensusXML')
                     
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 parameters 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/doxygen/nightly/html/TOPP_FeatureLinkerLabeled.html

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+FeatureLinkerLabeledGroups corresponding isotope-labeled features in a feature map.

version3.3.0-pre-nightly-2024-11-20 Version of the tool that generated this parameters file.

++1Instance '1' section for 'FeatureLinkerLabeled'

in Input fileinput file*.featureXML

out Output fileoutput file*.consensusXML

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue, false

forcefalse Overrides tool-specific checkstrue, false

testfalse Enables the test mode (needed for internal use only)true, false

+++algorithmAlgorithm parameters section

rt_estimatetrue If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance. Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance.true, false

rt_pair_dist-20.0 optimal pair distance in RT [sec] from light to heavy feature

rt_dev_low15.0 maximum allowed deviation below optimal retention time distance0.0:∞

rt_dev_high15.0 maximum allowed deviation above optimal retention time distance0.0:∞

mz_pair_dists[4.0] optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3, .. by division through charge)

mz_dev0.05 maximum allowed deviation from optimal m/z distance
0.0:∞

mrmfalse this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)true, false