Web Documentation for MRMTransitionGroupPicker
Version of the tool that generated this parameters file.
Name of log file (created only when specified)
Sets the debug level
Sets the number of threads allowed to be used by the TOPP tool
Disables progress logging to command line
Overwrite tool specific checks.
Enables the test mode (needed for internal use only)
Stop finding after feature (ordered by intensity; -1 means do not stop).
Stop after reaching intensity ratio
Minimal peak width (s), discard all peaks below this value (-1 means no action).
Try to apply a background subtraction to the peak (experimental). The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that.
Tries to get better peak picking by looking at peak consistency of all picked peaks. Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large.
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).
Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold
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.
The number of subsequent data points used for smoothing.
This number has to be uneven. If it is not, 1 will be added.
Order of the polynomial that is fitted.
Gaussian width in seconds, estimated peak size.
Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)
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 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.
Signal to noise window length.
Signal to noise bin count.
Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin
Try to remove overlapping peaks during peak picking
Which method to choose for chromatographic peak-picking (OpenSWATH legacy, corrected picking or Crawdad).