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PeakPickerHiRes

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

pot. predecessor tools → PeakPickerHiRes → 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.

TOPP_example_signalprocessing_parameters is explained in the TOPP tutorial.

The command line parameters of this tool are:

INI file documentation of this tool:

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

Be aware that applying the algorithm to already picked data results in an error message and program exit or corrupted output data. Advanced users may skip the check for already centroided data using the flag "-force" (useful e.g. if spectrum annotations in the data files are wrong).

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