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.

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.)

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