PeakPickerMaxima

class pyopenms.PeakPickerMaxima

Bases: object

Cython implementation of _PeakPickerMaxima

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1PeakPickerMaxima.html

This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-MS, Orbitrap). In high resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width —– This peak-picking algorithm detects ion signals in raw data and reconstructs the corresponding peak shape by cubic spline interpolation. Signal detection depends on the signal-to-noise ratio which is adjustable by the user (see parameter signal_to_noise). A picked peak’s m/z and intensity value is given by the maximum of the underlying peak spline —– So far, this peak picker was mainly tested on high resolution data. With appropriate preprocessing steps (e.g. noise reduction and baseline subtraction), it might be also applied to low resolution data

__init__()

  • Cython signature: void PeakPickerMaxima(double signal_to_noise, double spacing_difference, double sn_window_length)

  • Cython signature: void PeakPickerMaxima(PeakPickerMaxima &)

Methods

__init__

  • Cython signature: void PeakPickerMaxima(double signal_to_noise, double spacing_difference, double sn_window_length)

findMaxima

Cython signature: void findMaxima(libcpp_vector[double] mz_array, libcpp_vector[double] int_array, libcpp_vector[PeakCandidate] & pc)

pick

Cython signature: void pick(libcpp_vector[double] mz_array, libcpp_vector[double] int_array, libcpp_vector[PeakCandidate] & pc)
findMaxima()

Cython signature: void findMaxima(libcpp_vector[double] mz_array, libcpp_vector[double] int_array, libcpp_vector[PeakCandidate] & pc)

Parameters

  • mz_array – The array containing m/z values

  • int_array – The array containing intensity values

  • pc – The resulting array containing the peak candidates

  • check_spacings – Check spacing constraints (recommended settings: yes for spectra, no for chromatograms)

pick()

Cython signature: void pick(libcpp_vector[double] mz_array, libcpp_vector[double] int_array, libcpp_vector[PeakCandidate] & pc)