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AccurateMassSearch

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

Match MS signals to molecules from a database by mass.

Web Documentation for AccurateMassSearch

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)
mass_error_value
Tolerance allowed for accurate mass search.
mass_error_unit
Unit of mass error (ppm or Da)
ionization_mode
Positive or negative ionization mode? If 'auto' is used, the first feature of the input map must contain the meta-value 'scan_polarity'. If its missing, the tool will exit with error.
isotopic_similarity
Computes a similarity score for each hit (only if the feature exhibits at least two isotopic mass traces).
use_feature_adducts
Whether to filter AMS candidates mismatching available feature adduct annotation.
keep_unidentified_masses
Keep features that did not yield any DB hit.
exportIsotopeIntensities
[featureXML input only] Export column with available isotope trace intensities (opt_global_MTint)

Input Ports

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featureXML or consensusXML file [featureXML,consensusXML]
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This file contains the list of potential positive adducts that will be looked for in the database. Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/PositiveAdducts.tsv in OpenMS/share is used. [tsv]
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This file contains the list of potential negative adducts that will be looked for in the database. Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/NegativeAdducts.tsv in OpenMS/share is used. [tsv]
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Database input file(s), containing three tab-separated columns of mass, formula, identifier. If 'mass' is 0, it is re-computed from the molecular sum formula. By default CHEMISTRY/HMDBMappingFile.tsv in OpenMS/share is used! If empty, the default will be used. [tsv]
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Database input file(s), containing four tab-separated columns of identifier, name, SMILES, INCHI.The identifier should match with mapping file. SMILES and INCHI are reported in the output, but not used otherwise. By default CHEMISTRY/HMDB2StructMapping.tsv in OpenMS/share is used! If empty, the default will be used. [tsv]

Output Ports

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mzTab file [mzTab]
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A copy of the input file, annotated with matching hits from the database. [featureXML,consensusXML]

Views

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

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

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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