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IDMapper

Generic Workflow Nodes for KNIME: OpenMS version 2.4.0.201810261314 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Assigns protein/peptide identifications to features or consensus features.

Web Documentation for IDMapper

Options

version
Version of the tool that generated this parameters file.
rt_tolerance
RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features. Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value.
mz_tolerance
m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features. Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value.
mz_measure
Unit of 'mz_tolerance'.
mz_reference
Source of m/z values for peptide identifications. If 'precursor', the precursor-m/z from the idXML is used. If 'peptide', masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches. ('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)
ignore_charge
For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) 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
Overwrite tool specific checks.
test
Enables the test mode (needed for internal use only)
use_centroid_rt
Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces.
use_centroid_mz
Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces. (If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)
use_subelements
Match using RT and m/z of sub-features instead of consensus RT and m/z. A consensus feature matches if any of its sub-features matches.
annotate_ids_with_subelements
Store the map index of the sub-feature in the peptide ID.

Input Ports

Protein/peptide identifications file [mzid,idXML]
Feature map/consensus map file [featureXML,consensusXML,mzq]
MS run used to annotated unidentified spectra to features or consensus features. [mzML,opt.]

Output Ports

Output file (the format depends on the input file format). [featureXML,consensusXML,mzq]

Views

IDMapper Std Output
The text sent to standard out during the execution of IDMapper.
IDMapper Error Output
The text sent to standard error during the execution of IDMapper. (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 Generic Workflow Nodes for KNIME: OpenMS from the following update site:

KNIME 3.7
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