Groups corresponding isotope-labeled features in a feature map.

potential predecessor tools	$\longrightarrow$ FeatureLinkerLabeled $\longrightarrow$	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/release/2.8.0/html/TOPP_FeatureLinkerLabeled.html
Version: 2.8.0 Feb 22 2022, 11:52:07, Revision: d203985
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:
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/release/2.8.0/html/TOPP_FeatureLinkerLabeled.html

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

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

version2.8.0 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