A tool for peak detection in profile data. Executes the peak picking with high_res algorithm.
pot. predecessor tools | ![]() ![]() | 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:
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 |