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. More...
#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakPickerMaxima.h>
Classes | |
struct | PeakCandidate |
The PeakCandidate describes the output of the peak picker. More... | |
Public Member Functions | |
PeakPickerMaxima (double signal_to_noise, double spacing_difference=1.5, double spacing_difference_gap=4.0, double sn_window_length=200, unsigned missing=2) | |
Constructor. More... | |
virtual | ~PeakPickerMaxima () |
Destructor. More... | |
void | findMaxima (const std::vector< double > &mz_array, const std::vector< double > &int_array, std::vector< PeakCandidate > &pc, bool check_spacings=true) |
Will find local maxima in raw data. More... | |
void | pick (std::vector< double > &mz_array, std::vector< double > &int_array, std::vector< PeakCandidate > &pc, bool check_spacings=true) |
Will pick peaks in a spectrum. More... | |
Protected Attributes | |
double | signal_to_noise_ |
double | sn_window_length_ |
double | spacing_difference_ |
double | spacing_difference_gap_ |
unsigned | missing_ |
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.
PeakPickerMaxima | ( | double | signal_to_noise, |
double | spacing_difference = 1.5 , |
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double | spacing_difference_gap = 4.0 , |
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double | sn_window_length = 200 , |
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unsigned | missing = 2 |
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Constructor.
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inlinevirtual |
Destructor.
void findMaxima | ( | const std::vector< double > & | mz_array, |
const std::vector< double > & | int_array, | ||
std::vector< PeakCandidate > & | pc, | ||
bool | check_spacings = true |
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) |
Will find local maxima in raw data.
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) |
void pick | ( | std::vector< double > & | mz_array, |
std::vector< double > & | int_array, | ||
std::vector< PeakCandidate > & | pc, | ||
bool | check_spacings = true |
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) |
Will pick peaks in a spectrum.
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) |
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OpenMS / TOPP release 2.0.0 | Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11 |