FeatureLinkerLabeled

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:

stty: 'standard input': Inappropriate ioctl for device

FeatureLinkerLabeled -- Groups corresponding isotope-labeled features in a feature map.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_FeatureLinkerLabeled.html
Version: 3.4.0-pre-nightly-2024-12-16 Dec 17 2024, 02:41:12, Revision: 96ad74c
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry 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 description 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.

version3.4.0-pre-nightly-2024-12-16 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