| OpenMS 2.5.0

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PeakPickerMaxima Class Reference
Analysis » PeakPicking

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_

## Detailed Description

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.

Parameters of this class are:

Name | Type | Default | Restrictions | Description
--- | --- | --- | --- | ---
signal_to_noise | float | 0.0 | min: 0.0 | Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)
spacing_difference_gap | float | 4.0 | min: 0.0 | The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. '0' to disable the constraint. Not applicable to chromatograms.
spacing_difference | float | 1.5 | min: 0.0 | Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points. If this difference is exceeded a missing point is assumed (see parameter 'missing'). A higher value implies a less stringent peak definition, since individual signals within the peak are allowed to be further apart. '0' to disable the constraint. Not applicable to chromatograms.
missing | int | 1 | min: 0 | Maximum number of missing points allowed when extending a peak to the left or to the right. A missing data point occurs if the spacing between two subsequent data points exceeds 'spacing_difference * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. Not applicable to chromatograms.
ms_levels | int list | [] | min: 1 | List of MS levels for which the peak picking is applied. If empty, auto mode is enabled, all peaks which aren't picked yet will get picked. Other scans are copied to the output without changes.
report_FWHM | string | false | true, false | Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak.
report_FWHM_unit | string | relative | relative, absolute | Unit of FWHM. Either absolute in the unit of input, e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms).
SignalToNoise:max_intensity | int | -1 | min: -1 | maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N.
SignalToNoise:auto_max_stdev_factor | float | 3.0 | min: 0.0 max: 999.0 | parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev
SignalToNoise:auto_max_percentile | int | 95 | min: 0 max: 100 | parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile
SignalToNoise:auto_mode | int | 0 | min: -1 max: 1 | method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method
SignalToNoise:win_len | float | 200.0 | min: 1.0 | window length in Thomson
SignalToNoise:bin_count | int | 30 | min: 3 | number of bins for intensity values
SignalToNoise:min_required_elements | int | 10 | min: 1 | minimum number of elements required in a window (otherwise it is considered sparse)
SignalToNoise:noise_for_empty_window | float | 1.0e20 |  | noise value used for sparse windows
SignalToNoise:write_log_messages | string | true | true, false | Write out log messages in case of sparse windows or median in rightmost histogram bin

Note:

- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.

Note
  The peaks must be sorted according to ascending m/z!

## Class Documentation

## ◆ OpenMS::PeakPickerMaxima::PeakCandidate

struct OpenMS::PeakPickerMaxima::PeakCandidate

The PeakCandidate describes the output of the peak picker.

It contains the m/z and intensity value of the peak candidate.

It also contains the original index in the m/z axis where the peak was found as well as an estimate of its right and left boundary.

Class Members
double | int_max | intensity value of the peak apex
int | left_boundary | index of the left boundary (relative to the input data)
double | mz_max | m/z value of the peak apex
int | pos | index of the peak apex (relative to the input data)
int | right_boundary | index of the right boundary (relative to the input data)

## Constructor & Destructor Documentation

## ◆ PeakPickerMaxima()

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.

## ◆ ~PeakPickerMaxima()

virtual ~PeakPickerMaxima | ( |  | ) |

inline virtual

Destructor.

## Member Function Documentation

## ◆ findMaxima()

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.

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)

Note
  This function will directly report peak apices with right and left boundaries but will not use any fitting to estimate the true m/z and intensity of the peak. Note that the mz_max and int_max fields will be empty in the result (set to -1).

## ◆ pick()

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.

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)

Note
  This function will first find maxima in the intensity domain and then use a spline function to estimate the best m/z and intensity for each peak candidate.

## Member Data Documentation

## ◆ missing_

unsigned missing_

protected

## ◆ signal_to_noise_

double signal_to_noise_

protected

## ◆ sn_window_length_

double sn_window_length_

protected

## ◆ spacing_difference_

double spacing_difference_

protected

## ◆ spacing_difference_gap_

double spacing_difference_gap_

protected