AccurateMassSearch

Match MS signals to molecules from a database by mass.

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.
id_format: Use legacy (ProteinID/PeptideID based storage of metabolomics data) with mzTab-v1.0.0 as output format or novel Identification Data (ID) with mzTab-v2.0.0-M as output format (ID and its MzTab-M output is currently only support for featureXML files).
exportIsotopeIntensities: [featureXML input only] Export column with available isotope trace intensities (opt_global_MTint)

: featureXML or consensusXML file [featureXML,consensusXML]
: 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]
: 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]
: 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]
: 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]

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

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.)

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To use this node in KNIME, install the extension OpenMS from the below update site following our NodePit Product and Node Installation Guide:

v5.3

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

Plugin provider: Freie Universitaet Berlin, Universitaet Tuebingen, ZIB (GKN-Team) and the OpenMS Team

Plugin version: 3.2.0.202409181756

On NodePit since: 2024-10-17

Last update: 2024-11-21

KNIME versions: v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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