Picks peaks in SRM/MRM chromatograms that belong to the same precursors.

potential predecessor tools	→ MRMTransitionGroupPicker →	potential successor tools
OpenSwathChromatogramExtractor		OpenSwathFeatureXMLToTSV
MRMMapper		OpenSwathFeatureXMLToTSV

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: find features (peaks) in individual chromatograms
Step 2: merge these features to consensus features that span multiple chromatograms

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

The command line parameters of this tool are:

MRMTransitionGroupPicker -- Picks peaks in SRM/MRM chromatograms.
Full documentation: http://www.openms.de/doxygen/release/3.0.0/html/UTILS_MRMTransitionGroupPicker.html
Version: 3.0.0 Jul 14 2023, 11:57:33, Revision: be787e9
To cite OpenMS:
 + Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for 
   mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.

Usage:
  MRMTransitionGroupPicker <options>

This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript
ion or use the --helphelp option

Options (mandatory options marked with '*'):
  -in <file>*        Input file (valid formats: 'mzML')
  -tr <file>*        Transition file ('TraML' or 'csv') (valid formats: 'csv', 'traML')
  -out <file>*       Output file (valid formats: 'featureXML')
                     
Common UTIL options:
  -ini <file>        Use the given TOPP INI file
  -threads <n>       Sets the number of threads allowed to be used by the TOPP tool (default: '1')
  -write_ini <file>  Writes the default configuration file
  --help             Shows options
  --helphelp         Shows all options (including advanced)

The following configuration subsections are valid:
 - algorithm   Algorithm parameters section

You can write an example INI file using the '-write_ini' option.
Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
For more information, please consult the online documentation for this tool:
  - http://www.openms.de/doxygen/release/3.0.0/html/UTILS_MRMTransitionGroupPicker.html

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+MRMTransitionGroupPickerPicks peaks in SRM/MRM chromatograms.

version3.0.0 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 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

++++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_width50.0 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