| OpenMS 2.5.0

MRMTransitionGroupPicker

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

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

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.

The command line parameters of this tool are:

    MRMTransitionGroupPicker -- Picks peaks in SRM/MRM chromatograms.

    Full documentation: http://www.openms.de/documentation/UTILS_MRMTransitionGroupPicker.html

    Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

    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/documentation/UTILS_MRMTransitionGroupPicker.html

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+MRMTransitionGroupPicker Picks peaks in SRM/MRM chromatograms.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'MRMTransitionGroupPicker'
in Input file input file*.mzML
tr transition file ('TraML' or 'csv')input file*.csv,*.traML
out output file output file*.featureXML
log Name of log file (created only when specified)
debug 0 Sets the debug level
threads 1 Sets the number of threads allowed to be used by the TOPP tool
no_progress false Disables progress logging to command line true,false
force false Overwrite tool specific checks.true,false
test false Enables the test mode (needed for internal use only)true,false
+++algorithm Algorithm parameters section
stop_after_feature-1 Stop finding after feature (ordered by intensity; -1 means do not stop).
stop_after_intensity_ratio 1.0e-04 Stop after reaching intensity ratio
min_peak_width-1.0 Minimal peak width (s), discard all peaks below this value (-1 means no action).
peak_integration original Calculate the peak area and height either the smoothed or the raw chromatogram data.original,smoothed
background_subtraction none 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_peaks false 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_precursors false Use precursor chromatogram for peak picking (note that this may lead to precursor signal driving the peak picking)true,false
use_consensus true Use consensus peak boundaries when computing transition group picking (if false, compute independent peak boundaries for each transition)true,false
recalculate_peaks_max_z 1.0 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-10000.0 Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold
resample_boundary 15.0 For computing peak quality, how many extra seconds should be sample left and right of the actual peak
compute_peak_quality false 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_metrics false Calculates various peak shape metrics (e.g., tailing) that can be used for downstream QC/QA.true,false
compute_total_mi false Compute mutual information metrics for individual transitions that can be used for OpenSWATH/IPF scoring.true,false
boundary_selection_method largest Method to use when selecting the best boundaries for peaks.largest,widest
++++PeakPickerMRM
sgolay_frame_length 15 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 3 Order of the polynomial that is fitted.
gauss_width 50.0 Gaussian width in seconds, estimated peak size.
use_gauss true 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_noise 1.0 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_len 1000.0 Signal to noise window length.
sn_bin_count 30 Signal to noise bin count.
write_sn_log_messages false Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin true,false
remove_overlapping_peaks false Try to remove overlapping peaks during peak picking false,true
method corrected 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_type intensity_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_type base_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_EMG false Fit the chromatogram/spectrum to the EMG peak model.false,true