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OpenSwathChromatogramExtractor

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

Extract chromatograms (XIC) from a MS2 map file.

Web Documentation for OpenSwathChromatogramExtractor

Options

version
Version of the tool that generated this parameters file.
min_upper_edge_dist
Minimal distance to the edge to still consider a precursor, in Thomson
rt_window
Extraction window in RT dimension (-1 means extract over the whole range). This is the full window size, e.g. a value of 1000 seconds would extract 500 seconds on either side.
ion_mobility_window
Extraction window in ion mobility dimension (in milliseconds). This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side.
mz_window
Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag). This is the full window size, e.g. 100 ppm would extract 50 ppm on either side.
ppm
m/z extraction_window is in ppm
is_swath
Set this flag if the data is SWATH data
extract_MS1
Extract the MS1 transitions based on the precursor values in the TraML file (useful for extracting MS1 XIC)
extraction_function
Function used to extract the signal
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)
type
Type of model
symmetric_regression
Only for 'linear' model: Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'.

Input Ports

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Input files separated by blank [mzML]
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transition file ('TraML' or 'csv') [csv,traML]
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RT normalization file (how to map the RTs of this run to the ones stored in the library) [trafoXML,opt.]

Output Ports

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output file [mzML]

Views

OpenSwathChromatogramExtractor Std Output
The text sent to standard out during the execution of OpenSwathChromatogramExtractor.
OpenSwathChromatogramExtractor Error Output
The text sent to standard error during the execution of OpenSwathChromatogramExtractor. (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 4.3

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

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Developers

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