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SpectraMerger

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

Merges spectra (each MS level separately), increasing S/N ratios.

Web Documentation for SpectraMerger

Options

version
Version of the tool that generated this parameters file.
merging_method
Method of merging which should be used.
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)
mz_binning_width
minimum m/z distance for two data points (profile data) or peaks (centroided data) to be considered distinct. Closer data points or peaks will be merged.
mz_binning_width_unit
Unit in which the distance between two data points or peaks is given.
sort_blocks
Sort blocks by <?> before merging them (useful for precursor order)
spectrum_type
Spectrum type of the MS level to be averaged
ms_level
Average spectra of this level. All other spectra remain unchanged.
rt_FWHM
FWHM of Gauss curve in seconds to be averaged over.
cutoff
Intensity cutoff for Gaussian. The Gaussian RT profile decreases from 1 at its apex to 0 at infinity. Spectra for which the intensity of the Gaussian drops below the cutoff do not contribute to the average.
spectrum_type
Spectrum type of the MS level to be averaged
ms_level
Average spectra of this level. All other spectra remain unchanged.
rt_range
RT range to be averaged over, i.e. +/-(RT range)/2 from each spectrum.
rt_unit
Unit for RT range.
ms_levels
Merge spectra of this level. All spectra with other MS levels remain untouched.
rt_block_size
Maximum number of scans to be summed up.
rt_max_length
Maximum RT size of the block in seconds (0.0 = no size restriction).
mz_tolerance
Max m/z distance of the precursor entries of two spectra to be merged in [Da].
rt_tolerance
Max RT distance of the precursor entries of two spectra to be merged in [s].

Input Ports

Input mzML file. [mzML]

Output Ports

Output mzML file with merged spectra. [mzML]

Views

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