IconDecharger0 ×

Generic Workflow Nodes for KNIME: OpenMS version 2.3.0.201712211252 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Decharges and merges different feature charge variants of the same peptide.

Web Documentation for Decharger

Options

version
Version of the tool that generated this parameters file.
log
Name of log file (created only when specified)
debug
Sets the debug level
threads
Sets the number of threads allowed to be used by the TOPP tool
no_progress
Disables progress logging to command line
force
Overwrite tool specific checks.
test
Enables the test mode (needed for internal use only)
charge_min
Minimal possible charge
charge_max
Maximal possible charge
charge_span_max
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 charge
q_try
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').
retention_max_diff
Maximum allowed RT difference between any two features if their relation shall be determined
retention_max_diff_local
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_diff
Maximum allowed mass difference [in Th] for a single feature.
potential_adducts
Adducts used to explain mass differences in format: 'Element(+)*:Probability[:RTShift[:Label]]', i.e. the number of '+' 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-4:1:-3' indicates a 4 deuterium label, which causes early elution by 3 seconds. As a fourth 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_neutrals
Maximal number of neutral adducts(q=0) allowed. Add them in the 'potential_adducts' section!
max_minority_bound
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 adduct
min_rt_overlap
Minimum overlap of the convex hull' RT intersection measured against the union from two features (if CHs are given)
intensity_filter
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.
default_map_label
Label of map in output consensus file where all features are put by default
verbose_level
Amount of debug information given during processing.

Input Ports

input file [featureXML]

Output Ports

output consensus map [consensusXML]
output feature map [featureXML,Inactive]
output file [consensusXML,Inactive]

Views

Decharger Std Output
The text sent to standard out during the execution of Decharger.
Decharger Error Output
The text sent to standard error during the execution of Decharger. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

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Update Site

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