Groups corresponding features from multiple maps using a QT clustering approach.
Reference:
Weisser et al.: An automated pipeline for high-throughput label-free quantitative proteomics (J. Proteome Res., 2013, PMID: 23391308).
This tool provides an algorithm for grouping corresponding features in multiple runs of label-free experiments. For more details and algorithm-specific parameters (set in the ini file) see "Detailed
Description" in the algorithm documentation".
FeatureLinkerUnlabeledQT takes several feature maps (featureXML files) 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 FeatureLinkerLabeled
The command line parameters of this tool are:
FeatureLinkerUnlabeledQT -- Groups corresponding features from multiple maps.
Version: 2.4.0 Oct 29 2018, 15:52:19, Revision: 9690d06
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:
FeatureLinkerUnlabeledQT <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 <files>* Input files separated by blanks (valid formats: 'featureXML', 'consensusXML')
-out <file>* Output file (valid formats: 'consensusXML')
-design <file> Input file containing the experimental design (valid formats: 'tsv')
-keep_subelements For consensusXML input only: If set, the sub-features of the inputs are transferred to
the output.
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.
Have a look at the OpenMS documentation for more information.
INI file documentation of this tool:
Legend:
required parameter
advanced parameter
+FeatureLinkerUnlabeledQTGroups corresponding features from multiple maps.
version2.4.0
Version of the tool that generated this parameters file.
++1Instance '1' section for 'FeatureLinkerUnlabeledQT'
in[]
input files separated by blanksinput file*.featureXML,*.consensusXML
out
Output fileoutput file*.consensusXML
design
input file containing the experimental designinput file*.tsv
keep_subelementsfalse
For consensusXML input only: If set, the sub-features of the inputs are transferred to the output.true,false
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
Overwrite tool specific checks.true,false
testfalse
Enables the test mode (needed for internal use only)true,false
+++algorithmAlgorithm parameters section
use_identificationsfalse
Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account).true,false
nr_partitions100
How many partitions in m/z space should be used for the algorithm (more partitions means faster runtime and more memory efficient execution )1:∞
ignore_chargefalse
false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge statetrue,false
ignore_adducttrue
true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adductstrue,false
++++distance_RTDistance component based on RT differences
max_difference100
Never pair features with a larger RT distance (in seconds).0:∞
exponent1
Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)0:∞
weight1
Final RT distances are weighted by this factor0:∞
++++distance_MZDistance component based on m/z differences
max_difference0.3
Never pair features with larger m/z distance (unit defined by 'unit')0:∞
unitDa
Unit of the 'max_difference' parameterDa,ppm
exponent2
Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)0:∞
weight1
Final m/z distances are weighted by this factor0:∞
++++distance_intensityDistance component based on differences in relative intensity (usually relative to highest peak in the whole data set)
exponent1
Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)0:∞
weight0
Final intensity distances are weighted by this factor0:∞
log_transformdisabled
Log-transform intensities? If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))enabled,disabled