Picks peaks in SRM/MRM chromatograms that belong to the same precursors.
This tools accepts a set of chromatograms and picks peaks in them, correctly grouping related transitions from the same precursor together. It will perform the following steps:
Step 1 is performed by smoothing the individual chromatogram and applying the PeakPickerHiRes.
Step 2 is performed by finding the largest peak overall and use this to create a feature, propagating this through all chromatograms.
This tool will not compute any scores for the peaks, in order to do peak picking please use TOPP_OpenSwathAnalyzer
Legend:
required parameter
advanced parameter
+MRMTransitionGroupPickerPicks peaks in SRM/MRM chromatograms.
version3.4.0-pre-nightly-2024-12-16
Version of the tool that generated this parameters file.
++1Instance '1' section for 'MRMTransitionGroupPicker'
in
Input fileinput file*.mzML
tr
transition file ('TraML' or 'csv')input file*.csv, *.traML
out
output fileoutput file*.featureXML
log
Name of log file (created only when specified)
debug0
Sets the debug level
threads1
Sets the number of threads allowed to be used by the TOPP tool
no_progressfalse
Disables progress logging to command linetrue, false
forcefalse
Overrides tool-specific checkstrue, false
testfalse
Enables the test mode (needed for internal use only)true, false
+++algorithmAlgorithm parameters section
stop_after_feature-1
Stop finding after feature (ordered by intensity; -1 means do not stop).
stop_after_intensity_ratio1.0e-04
Stop after reaching intensity ratio
min_peak_width1.0e-03
Minimal peak width (s), discard all peaks below this value (-1 means no action).
peak_integrationoriginal
Calculate the peak area and height either the smoothed or the raw chromatogram data.original, smoothed
background_subtractionnone
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.none, original, exact
recalculate_peaksfalse
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.true, false
use_precursorsfalse
Use precursor chromatogram for peak picking (note that this may lead to precursor signal driving the peak picking)true, false
use_consensustrue
Use consensus peak boundaries when computing transition group picking (if false, compute independent peak boundaries for each transition)true, false
recalculate_peaks_max_z1.0
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-1.0e04
Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold
resample_boundary15.0
For computing peak quality, how many extra seconds should be sample left and right of the actual peak
compute_peak_qualityfalse
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.true, false
compute_peak_shape_metricsfalse
Calculates various peak shape metrics (e.g., tailing) that can be used for downstream QC/QA.true, false
compute_total_mifalse
Compute mutual information metrics for individual transitions that can be used for OpenSWATH/IPF scoring.true, false
boundary_selection_methodlargest
Method to use when selecting the best boundaries for peaks.largest, widest
++++PeakPickerChromatogram
sgolay_frame_length15
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_order3
Order of the polynomial that is fitted.
gauss_width50.0
Gaussian width in seconds, estimated peak size.
use_gausstrue
Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)false, true
peak_width-1.0
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_noise1.0
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.0.0:∞
sn_win_len1000.0
Signal to noise window length.
sn_bin_count30
Signal to noise bin count.
write_sn_log_messagesfalse
Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bintrue, false
remove_overlapping_peaksfalse
Try to remove overlapping peaks during peak pickingfalse, true
methodcorrected
Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram).legacy, corrected, crawdad
++++PeakIntegrator
integration_typeintensity_sum
The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration.intensity_sum, simpson, trapezoid
baseline_typebase_to_base
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).base_to_base, vertical_division, vertical_division_min, vertical_division_max
fit_EMGfalse
Fit the chromatogram/spectrum to the EMG peak model.false, true
1.9.1