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ClusterMassTracesByPrecursor

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

Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile.

Web Documentation for ClusterMassTracesByPrecursor

Options

version
Version of the tool that generated this parameters file.
assign_unassigned_to_all
Assign unassigned MS2 fragments to all precursors (only for ms1_centrif)
min_pearson_correlation
Minimal pearson correlation score to match elution profiles to each other.
max_lag
Maximal lag (e.g. by how many spectra the peak may be shifted at most). This parameter will depend on your chromatographic setup but a number between 1 and 3 is usually sensible.
min_nr_ions
Minimal number of ions to report a spectrum.
max_rt_apex_difference
Maximal difference of the apex in retention time (in seconds). This is a hard parameter, all profiles further away will not be considered at all.
swath_lower
Swath lower isolation window
swath_upper
Swath upper isolation window
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)

Input Ports

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MS1 mass traces [consensusXML]
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MS2 / SWATH mass traces [consensusXML]

Output Ports

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output file [mzML]

Views

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

Best Friends (Outgoing)

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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