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EICExtractor

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

Extracts intensities from dedicates positions in a LC/MS map

Web Documentation for EICExtractor

Options

version
Version of the tool that generated this parameters file.
rt_tol
RT tolerance in [s] for finding max peak (whole RT range around RT middle)
mz_tol
m/z tolerance in [ppm] for finding a peak
rt_collect
# of scans up & down in RT from highest point for ppm estimation in result
out_separator
Separator character for output CSV 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
Overwrite tool specific checks.
test
Enables the test mode (needed for internal use only)
enabled
Automatically detect injection peaks from TIC and quantify all m/z x RT combinations.
FHWM
Expected full width at half-maximum of each raw RT peak in [s]. Gaussian smoothing filter with this width is applied to TIC.
SNThreshold
S/N threshold for a smoothed raw peak to pass peak picking. Higher thesholds will result in less peaks.

Input Ports

Input raw data file [mzML]
[for Waters data only] Read additional information from _HEADER.TXT. Provide one for each raw input file. [txt,opt.]
Input config file stating where to find signal [edta]

Output Ports

Output quantitation file (multiple columns for each input compound) [csv]
Optional output file (for first input) containing the smoothed TIC, S/N levels and picked RT positions [mzML,Inactive]

Views

EICExtractor Std Output
The text sent to standard out during the execution of EICExtractor.
EICExtractor Error Output
The text sent to standard error during the execution of EICExtractor. (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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Update Site

To use this node in KNIME, install Generic Workflow Nodes for KNIME: OpenMS from the following update site:

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