OpenMS  3.0.0
Decharger

Decharges a feature map by clustering charge variants of a peptide to zero-charge entities.

pot. predecessor tools $ \longrightarrow $ Decharger $ \longrightarrow $ pot. successor tools
FeatureFinderCentroided ProteinQuantifier

The Decharger uses an ILP approach to group charge variants of the same peptide, which usually occur in ESI ionization mode. The resulting zero-charge peptides, which are defined by RT and mass, are written to consensusXML. Intensities of charge variants are summed up. The position of the zero charge variant is the average of all clustered peptides in each dimension (m/z and RT). It is also possible to include adducted species to the charge ladders (see 'potential_adducts' parameter). Via this mechanism it is also possible to use this tool to find pairs/triples/quadruples/... in labeled data (by specifing the mass tag weight as an adduct). If mass tags induce an RT shift (e.g. deuterium labeled data) you can also specify this also in the adduct list. This will allow to tighten the RT search window, thus reducing false positive results.

This tool is described in the following publication:

Bielow C, Ruzek S, Huber CG, Reinert K. Optimal decharging and clustering of charge ladders generated in ESI-MS. J Proteome Res 2010; 9: 2688.
DOI: 10.1021/pr100177k

The command line parameters of this tool are:

Decharger -- Decharges and merges different feature charge variants of the same peptide.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_Decharger.html
Version: 3.0.0-pre-nightly-2022-07-20 Jul 21 2022, 00:07:28, Revision: ea0316e
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.
To cite Decharger:
  Bielow C, Ruzek S, Huber CG, Reinert K. Optimal decharging and clustering of charge ladders generated in ESI-MS. J Proteome Res 2010; 9: 2688. doi:10.1021/pr100177k.

Usage:
  Decharger <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_cm <file>*    Output consensus map (valid formats: 'consensusXML')
  -out_fm <file>     Output feature map (valid formats: 'featureXML')
  -outpairs <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   Feature decharging 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/doxygen/nightly/html/TOPP_Decharger.html

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+DechargerDecharges and merges different feature charge variants of the same peptide.
version3.0.0-pre-nightly-2022-07-20 Version of the tool that generated this parameters file.
++1Instance '1' section for 'Decharger'
in input file input file*.featureXML
out_cm output consensus mapoutput file*.consensusXML
out_fm output feature mapoutput file*.featureXML
outpairs 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
+++algorithmFeature decharging algorithm section
++++FeatureDeconvolution
charge_min1 Minimal possible charge
charge_max10 Maximal possible charge
charge_span_max4 Maximal range of charges for a single analyte, i.e. observing q1=[5,6,7] implies span=3. Setting this to 1 will only find adduct variants of the same charge1:∞
q_tryfeature Try different values of charge for each feature according to the above settings ('heuristic' [does not test all charges, just the likely ones] or 'all' ), or leave feature charge untouched ('feature').feature,heuristic,all
retention_max_diff1.0 Maximum allowed RT difference between any two features if their relation shall be determined
retention_max_diff_local1.0 Maximum allowed RT difference between between two co-features, after adduct shifts have been accounted for (if you do not have any adduct shifts, this value should be equal to 'retention_max_diff', otherwise it should be smaller!)
mass_max_diff0.5 Maximum allowed mass difference [in Th] for a single feature.
potential_adducts[K:+:0.1] Adducts used to explain mass differences in format: 'Element:Charge(+/-):Probability[:RTShift[:Label]]', i.e. the number of '+' or '-' indicate the charge, e.g. 'Ca:++:0.5' indicates +2. Probabilites have to be in (0,1]. RTShift param is optional and indicates the expected RT shift caused by this adduct, e.g. '(2)H4H-4:0:1:-3' indicates a 4 deuterium label, which causes early elution by 3 seconds. As a fifth parameter you can add a label which is tagged on every feature which has this adduct. This also determines the map number in the consensus file.
max_neutrals0 Maximal number of neutral adducts(q=0) allowed. Add them in the 'potential_adducts' section!
max_minority_bound2 Maximum count of the least probable adduct (according to 'potential_adducts' param) within a charge variant. E.g. setting this to 2 will not allow an adduct composition of '1(H+),3(Na+)' if Na+ is the least probable adduct0:∞
min_rt_overlap0.66 Minimum overlap of the convex hull' RT intersection measured against the union from two features (if CHs are given)0.0:1.0
intensity_filterfalse Enable the intensity filter, which will only allow edges between two equally charged features if the intensity of the feature with less likely adducts is smaller than that of the other feature. It is not used for features of different charge.true,false
negative_modefalse Enable negative ionization mode.
default_map_labeldecharged features Label of map in output consensus file where all features are put by default
verbose_level0 Amount of debug information given during processing.0:3