AssayGeneratorMetabo

Options

version

Version of the tool that generated this parameters file.

ambiguity_resolution_mz_tolerance

Mz tolerance for the resolution of identification ambiguity over multiple files

ambiguity_resolution_mz_tolerance_unit

Unit of the ambiguity_resolution_mz_tolerance

ambiguity_resolution_rt_tolerance

RT tolerance in seconds for the resolution of identification ambiguity over multiple files

total_occurrence_filter

Filter compound based on total occurrence in analysed samples

method

Spectrum with the highest precursor intensity or a consensus spectrum is used for assay library construction (if no fragment annotation is used).

exclude_ms2_precursor

Excludes precursor in ms2 from transition list

use_known_unknowns

Use features without identification information

min_transitions

Minimal number of transitions

max_transitions

Maximal number of transitions

cosine_similarity_threshold

Threshold for cosine similarity of MS2 spectra from the same precursor used in consensus spectrum creation

transition_threshold

Further transitions need at least x% of the maximum intensity (default 5%)

min_fragment_mz

Minimal m/z of a fragment ion choosen as a transition

max_fragment_mz

Maximal m/z of a fragment ion choosen as a transition

precursor_mz_distance

Max m/z distance of the precursor entries of two spectra to be merged in [Da].

precursor_recalibration_window

Tolerance window for precursor selection (Annotation of precursor mz and intensity)

precursor_recalibration_window_unit

Unit of the precursor_mz_tolerance_annotation

precursor_consensus_spectrum_rt_tolerance

Tolerance window (left and right) for precursor selection [seconds], for consensus spectrum generation (only available without fragment annotation)

deisotoping_use_deisotoper

Use Deisotoper (if no fragment annotation is used)

deisotoping_fragment_tolerance

Tolerance used to match isotopic peaks

deisotoping_fragment_unit

Unit of the fragment tolerance

deisotoping_min_charge

The minimum charge considered

deisotoping_max_charge

The maximum charge considered

deisotoping_min_isopeaks

The minimum number of isotopic peaks (at least 2) required for an isotopic cluster

deisotoping_max_isopeaks

The maximum number of isotopic peaks (at least 2) considered for an isotopic cluster

deisotoping_keep_only_deisotoped

Only monoisotopic peaks of fragments with isotopic pattern are retained

deisotoping_annotate_charge

Annotate the charge to the peaks

filter_by_num_masstraces

Number of mass traces each feature has to have to be included. To use this parameter, setting the feature_only flag is necessary

precursor_mz_tolerance

Tolerance window for precursor selection (Feature selection in regard to the precursor)

precursor_mz_tolerance_unit

Unit of the preprocessing_precursor_mz_tolerance

precursor_rt_tolerance

Tolerance window (left and right) for precursor selection [seconds]

feature_only

Uses the feature information from in_featureinfo to reduce the search space to MS2 associated with a feature

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)

Views

AssayGeneratorMetabo Std Output

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

AssayGeneratorMetabo Error Output

The text sent to standard error during the execution of AssayGeneratorMetabo. (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

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