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.
Legend:
required parameter
advanced parameter
+MRMTransitionGroupPickerPicks peaks in SRM/MRM chromatograms.
version2.3.0
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
Overwrite tool specific checks.true,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_ratio0.0001
Stop after reaching intensity ratio
min_peak_width-1
Minimal peak width (s), discard all peaks below this value (-1 means no action).
background_subtractionnone
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.none,smoothed,original
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 theof variation within the picked peaks is too large.true,false
use_precursorsfalse
Use precursor chromatogram for peak pickingtrue,false
recalculate_peaks_max_z1
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-10000
Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold
resample_boundary15
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
++++PeakPickerMRM
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
Gaussian width in seconds, estimated peak size.
use_gausstrue
Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)false,true
peak_width-1
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
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:∞
sn_win_len1000
Signal to noise window length.
sn_bin_count30
Signal to noise bin count.
write_sn_log_messagestrue
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