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PeakPickerHiRes

A tool for peak detection in profile data. Executes the peak picking with high_res algorithm.

pot. predecessor tools $ \longrightarrow $ PeakPickerHiRes $ \longrightarrow $ pot. successor tools
BaselineFilter any tool operating on MS peak data
(in mzML format)
NoiseFilterGaussian
NoiseFilterSGolay

Reference:
Weisser et al.: An automated pipeline for high-throughput label-free quantitative proteomics (J. Proteome Res., 2013, PMID: 23391308).

The conversion of the "raw" ion count data acquired by the machine into peak lists for further processing is usually called peak picking or centroiding. The choice of the algorithm should mainly depend on the resolution of the data. As the name implies, the high_res algorithm is fit for high resolution (orbitrap or FTICR) data.

Finding the right parameters for the is explained in the TOPP tutorial.

The command line parameters of this tool are:

PeakPickerHiRes -- Finds mass spectrometric peaks in profile mass spectra.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976

Usage:
  PeakPickerHiRes <options>

This tool has algoritm parameters that are not shown here! Please check the ini file for a detailed descripti
on or use the --helphelp option.

Options (mandatory options marked with '*'):
  -in <file>*        Input profile data file  (valid formats: 'mzML')
  -out <file>*       Output peak file  (valid formats: 'mzML')
                     
Common TOPP 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
+PeakPickerHiResFinds mass spectrometric peaks in profile mass spectra.
version1.11.1 Version of the tool that generated this parameters file.
++1Instance '1' section for 'PeakPickerHiRes'
in input profile data file input file*.mzML
out output peak file output file*.mzML
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
testfalse Enables the test mode (needed for internal use only)true,false
+++algorithmAlgorithm parameters section
signal_to_noise1 Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)0:∞
ms1_onlyfalse If true, peak picking is only applied to MS1 scans. Other scans are copied to the output without changes.true,false

For the parameters of the algorithm section see the algorithm documentation: PeakPickerHiRes

In the following table you, can find example values of the most important algorithm parameters for different instrument types.
These parameters are not valid for all instruments of that type, but can be used as a starting point for finding suitable parameters.

  Q-TOF LTQ Orbitrap
signal_to_noise 2 0

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5