MetaboliteAdductDecharger

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

Overrides 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 tolerance per feature. Defines a symmetric tolerance window around the feature. When looking at possible feature pairs, the allowed feature-wise errors are combined for consideration of possible adduct shifts. For ppm tolerances, each window is based on the respective observed feature mz (instead of putative experimental mzs causing the observed one)!

unit

Unit of the 'max_difference' parameter

potential_adducts

Adducts used to explain mass differences in format: 'Elements:Charge(+/-/0):Probability[:RTShift[:Label]]', i.e. the number of '+' or '-' indicate the charge ('0' if neutral adduct), e.g. 'Ca:++:0.5' indicates +2. Probabilites have to be in (0,1]. The optional RTShift param 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 fifth parameter you can add a label for every feature with this adduct. This also determines the map number in the consensus file. Adduct element losses are written in the form 'H-2'. All provided adducts need to have the same charge sign or be neutral! Mixing of adducts with different charge directions is only allowed as neutral complexes. For example, 'H-1Na:0:0.05' can be used to model Sodium gains (with balancing deprotonation) in negative mode.

max_neutrals

Maximal number of neutral adducts(q=0) allowed. Add them in the 'potential_adducts' section!

use_minority_bound

Prune the considered adduct transitions by transition probabilities.

max_minority_bound

Limits allowed adduct compositions and changes between compositions in the underlying graph optimization problem by introducing a probability-based threshold: the minority bound sets the maximum count of the least probable adduct (according to 'potential_adducts' param) within a charge variant with maximum charge only containing the most likely adduct otherwise. E.g., for 'charge_max' 4 and 'max_minority_bound' 2 with most probable adduct being H+ and least probable adduct being Na+, this will allow adduct compositions of '2(H+),2(Na+)' but not of '1(H+),3(Na+)'. Further, adduct compositions/changes less likely than '2(H+),2(Na+)' will be discarded as well.

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.

negative_mode

Enable negative ionization mode.

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.

Views

MetaboliteAdductDecharger Std Output

The text sent to standard out during the execution of MetaboliteAdductDecharger.

MetaboliteAdductDecharger Error Output

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

Workflows

• DIAMetAlyzer_2.0OpenMS
• DIAMetAlyzer_2.0KNIME Hub
• DIAMetAlyzer_ABKNIME Forum
• KNIME_GNPSExportKNIME Hub
• Metabolite_Adduct_GroupingOpenMS
• Show all 9 workflows

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