EICExtractor

Extracts intensities from dedicates positions in a LC/MS map

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: Overrides 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 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 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]

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

v5.2

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: 3.0.0.202307112039

On NodePit since: 2023-12-06

Last update: 2024-04-18

KNIME versions: 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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