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PeakPickerIterative

Generic Workflow Nodes for KNIME: OpenMS version 2.5.0.202002201806 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Finds mass spectrometric peaks in profile mass spectra.

Web Documentation for PeakPickerIterative

Options

version
Version of the tool that generated this parameters 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)
signal_to_noise_
Signal to noise value, each peak is required to be above this value (turn off by setting it to 0.0)
peak_width
Expected peak width half width in Dalton - peaks will be extended until this half width is reached (even if the intensitity is increasing). In conjunction with check_width_internally it will also be used to remove peaks whose spacing is larger than this value.
spacing_difference
Difference between peaks in multiples of the minimal difference to continue. The higher this value is set, the further apart peaks are allowed to be to still extend a peak. E.g. if the value is set to 1.5 and in a current peak the minimal spacing between peaks is 10 mDa, then only peaks at most 15 mDa apart will be added to the peak.
sn_bin_count_
Bin count for the Signal to Noise estimation.
nr_iterations_
Nr of iterations to perform (how many times the peaks are re-centered).
sn_win_len_
Window length for the Signal to Noise estimation.
check_width_internally
Delete peaks where the spacing is larger than the peak width (should be set to true to avoid artefacts)
ms1_only
Only do MS1
clear_meta_data
Delete meta data about peak width

Input Ports

Icon
input file [mzML]

Output Ports

Icon
output file [mzML]

Views

PeakPickerIterative Std Output
The text sent to standard out during the execution of PeakPickerIterative.
PeakPickerIterative Error Output
The text sent to standard error during the execution of PeakPickerIterative. (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 4.2
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