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AssayGeneratorMetabo

Generic Workflow Nodes for KNIME: OpenMS version 2.6.0.202009301213 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Assay library generation from DDA data (Metabolomics)

Web Documentation for AssayGeneratorMetabo

Options

version
Version of the tool that generated this parameters file.
fragment_annotation
Fragment annotation method
method
Spectrum with the highest precursor intensity or a consensus spectrum ist used for assay library construction (if no fragment annotation is used).
use_exact_mass
Use exact mass for fragment annotation
exclude_ms2_precursor
Excludes precursor in ms2 from transition list
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_rt_tolerance
Tolerance window (left and right) for precursor selection [seconds]
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
out_workspace_directory
Output directory for SIRIUS workspace
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)
use_deisotoper
Use Deisotoper (if no fragment annotation is used)
fragment_tolerance
Tolerance used to match isotopic peaks
fragment_unit
Unit of the fragment tolerance
min_charge
The minimum charge considered
max_charge
The maximum charge considered
min_isopeaks
The minimum number of isotopic peaks (at least 2) required for an isotopic cluster
max_isopeaks
The maximum number of isotopic peaks (at least 2) considered for an isotopic cluster
keep_only_deisotoped
Only monoisotopic peaks of fragments with isotopic pattern are retained
annotate_charge
Annotate the charge to the peaks
filter_by_num_masstraces
Features have to have at least x MassTraces. To use this parameter feature_only is neccessary
precursor_mz_tolerance
Tolerance window for precursor selection (Feature selection in regard to the precursor)
precursor_mz_tolerance_unit
Unit of the precursor_mz_tolerance
precursor_rt_tolerance
Tolerance window (left and right) for precursor selection [seconds]
isotope_pattern_iterations
Number of iterations that should be performed to extract the C13 isotope pattern. If no peak is found (C13 distance) the function will abort. Be careful with noisy data - since this can lead to wrong isotope patterns.
feature_only
Uses the feature information from in_featureinfo to reduce the search space to MS2 associated with a feature.
no_masstrace_info_isotope_pattern
Use this flag if the masstrace information from a feature should be discarded and the isotope_pattern_iterations should be used instead.
profile
Specify the used analysis profile
candidates
The number of candidates in the SIRIUS output.
database
search formulas in given database
noise
median intensity of noise peaks
ppm_max
allowed ppm for decomposing masses
isotope
how to handle isotope pattern data. Use 'score' to use them for ranking or 'filter' if you just want to remove candidates with bad isotope pattern. With 'both' you can use isotopes for filtering and scoring. Use 'omit' to ignore isotope pattern.
elements
The allowed elements. Write CHNOPSCl to allow the elements C, H, N, O, P, S and Cl. Add numbers in brackets to restrict the maximal allowed occurrence of these elements: CHNOP[5]S[8]Cl[1].
compound_timeout
Time out in seconds per compound. To disable the timeout set the value to 0
tree_timeout
Time out in seconds per fragmentation tree computation.
top_n_hits
The number of top hits for each compound written to the CSI:FingerID output
cores
The number of cores SIRIUS is allowed to use on the system
auto_charge
Use this option if the charge of your compounds is unknown and you do not want to assume [M+H]+ as default. With the auto charge option SIRIUS will not care about charges and allow arbitrary adducts for the precursor peak.
ion_tree
Print molecular formulas and node labels with the ion formula instead of the neutral formula
no_recalibration
If this option is set, SIRIUS will not recalibrate the spectrum during the analysis.
most_intense_ms2
SIRIUS uses the fragmentation spectrum with the most intense precursor peak (for each spectrum)

Input Ports

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SIRIUS executable e.g. sirius [,opt.]
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MzML input file(s) used for assay library generation [mzML]
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FeatureXML input file(s) containing identification information (e.g. AccurateMassSearch) [featureXML]

Output Ports

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Assay library output file [tsv,traML,pqp]

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.)

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Installation

To use this node in KNIME, install OpenMS from the following update site:

KNIME 4.2

A zipped version of the software site can be downloaded here.

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Developers

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