MRMTransitionGroupPicker

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

potential predecessor tools	$\longrightarrow$ MRMTransitionGroupPicker $\longrightarrow$	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.
Version: 2.3.0 Jan  9 2018, 17:46:23, Revision: 38ae115

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.
Have a look at the OpenMS documentation for more information.

INI file documentation of this tool:

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