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MRMTransitionGroupPicker

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

Picks peaks in SRM/MRM chromatograms.

Web Documentation for MRMTransitionGroupPicker

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
Overrides tool-specific checks
test
Enables the test mode (needed for internal use only)
stop_after_feature
Stop finding after feature (ordered by intensity; -1 means do not stop).
stop_after_intensity_ratio
Stop after reaching intensity ratio
min_peak_width
Minimal peak width (s), discard all peaks below this value (-1 means no action).
peak_integration
Calculate the peak area and height either the smoothed or the raw chromatogram data.
background_subtraction
Remove background from peak signal using estimated noise levels. The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation.
recalculate_peaks
Tries to get better peak picking by looking at peak consistency of all picked peaks. Tries to use the consensus (median) peak border if the variation within the picked peaks is too large.
use_precursors
Use precursor chromatogram for peak picking (note that this may lead to precursor signal driving the peak picking)
use_consensus
Use consensus peak boundaries when computing transition group picking (if false, compute independent peak boundaries for each transition)
recalculate_peaks_max_z
Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries. If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0).
minimal_quality
Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold
resample_boundary
For computing peak quality, how many extra seconds should be sample left and right of the actual peak
compute_peak_quality
Tries to compute a quality value for each peakgroup and detect outlier transitions. The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad.
compute_peak_shape_metrics
Calculates various peak shape metrics (e.g., tailing) that can be used for downstream QC/QA.
compute_total_mi
Compute mutual information metrics for individual transitions that can be used for OpenSWATH/IPF scoring.
boundary_selection_method
Method to use when selecting the best boundaries for peaks.
sgolay_frame_length
The number of subsequent data points used for smoothing. This number has to be uneven. If it is not, 1 will be added.
sgolay_polynomial_order
Order of the polynomial that is fitted.
gauss_width
Gaussian width in seconds, estimated peak size.
use_gauss
Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)
peak_width
Force a certain minimal peak_width on the data (e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off.
signal_to_noise
Signal-to-noise threshold at which a peak will not be extended any more. Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured.
sn_win_len
Signal to noise window length.
sn_bin_count
Signal to noise bin count.
write_sn_log_messages
Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin
remove_overlapping_peaks
Try to remove overlapping peaks during peak picking
method
Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram).
integration_type
The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration.
baseline_type
The baseline type to use in estimateBackground() based on the peak boundaries. A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base).
fit_EMG
Fit the chromatogram/spectrum to the EMG peak model.

Input Ports

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Input file [mzML]
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transition file ('TraML' or 'csv') [csv,traML]

Output Ports

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output file [featureXML]

Views

MRMTransitionGroupPicker Std Output
The text sent to standard out during the execution of MRMTransitionGroupPicker.
MRMTransitionGroupPicker Error Output
The text sent to standard error during the execution of MRMTransitionGroupPicker. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install OpenMS from the following update site:

KNIME 4.2
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