| OpenMS 2.5.0

Static Public Member Functions | List of all members
OPXLSpectrumProcessingAlgorithms Class Reference

`#include <OpenMS/ANALYSIS/XLMS/OPXLSpectrumProcessingAlgorithms.h>`

## Static Public Member Functions

static PeakSpectrum | mergeAnnotatedSpectra (PeakSpectrum &first_spectrum, PeakSpectrum &second_spectrum)
| Merges two spectra into one while correctly considering metainfo in DataArrays. More...
static PeakMap | preprocessSpectra (PeakMap &exp, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, Size peptide_min_size, Int min_precursor_charge, Int max_precursor_charge, bool deisotope, bool labeled)
| Preprocesses spectra. More...
static void | getSpectrumAlignmentFastCharge (std::vector< std::pair< Size, Size > > &alignment, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &theo_spectrum, const PeakSpectrum &exp_spectrum, const DataArrays::IntegerDataArray &theo_charges, const DataArrays::IntegerDataArray &exp_charges, DataArrays::FloatDataArray &ppm_error_array, double intensity_cutoff=0.0)
| Computes a spectrum alignment while considering fragment charges stored in a IntegerDataArray and a cut-off for the intensity difference ratio. More...
static void | getSpectrumAlignmentSimple (std::vector< std::pair< Size, Size > > &alignment, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const std::vector< SimpleTSGXLMS::SimplePeak > &theo_spectrum, const PeakSpectrum &exp_spectrum, const DataArrays::IntegerDataArray &exp_charges)
| Computes a spectrum alignment while considering fragment charges. Uses TSGXLMS::SimplePeak for the theoretical spectrum and its charges. Does not consider intensities. More...

## Member Function Documentation

## ◆ getSpectrumAlignmentFastCharge()

static void getSpectrumAlignmentFastCharge | ( | std::vector< std::pair< Size, Size > > & | alignment,
|  | double | fragment_mass_tolerance,
|  | bool | fragment_mass_tolerance_unit_ppm,
|  | const PeakSpectrum & | theo_spectrum,
|  | const PeakSpectrum & | exp_spectrum,
|  | const DataArrays::IntegerDataArray & | theo_charges,
|  | const DataArrays::IntegerDataArray & | exp_charges,
|  | DataArrays::FloatDataArray & | ppm_error_array,
|  | double | intensity_cutoff = `0.0`
| ) |  |

static

Computes a spectrum alignment while considering fragment charges stored in a IntegerDataArray and a cut-off for the intensity difference ratio.

Parameters

  alignment | The empty alignment, that will be filled by the algorithm
  fragment_mass_tolerance | The peak mass tolerance
  fragment_mass_tolerance_unit_ppm | True if the given tolerance is a ppm tolerance, false if tolerance is in Da
  theo_spectrum | The first spectrum to be aligned (preferably the theoretical one)
  exp_spectrum | the second spectrum to be aligned (preferably the experimental one)
  theo_charges | IntegerDataArray with charges for the theo_spectrum
  exp_charges | IntegerDataArray with charges for the exp_spectrum
  ppm_error_array | empty FloatDataArray to be filled with per peak ppm errors
  intensity_cutoff | Peaks will only be aligned if intensity1 / intensity2 > intensity_cutoff, with intensity1 being the lower of the two compared peaks and intensity2 the higher one. Set to 0 to ignore intensity differences.

## ◆ getSpectrumAlignmentSimple()

static void getSpectrumAlignmentSimple | ( | std::vector< std::pair< Size, Size > > & | alignment,
|  | double | fragment_mass_tolerance,
|  | bool | fragment_mass_tolerance_unit_ppm,
|  | const std::vector< SimpleTSGXLMS::SimplePeak > & | theo_spectrum,
|  | const PeakSpectrum & | exp_spectrum,
|  | const DataArrays::IntegerDataArray & | exp_charges
| ) |  |

static

Computes a spectrum alignment while considering fragment charges. Uses TSGXLMS::SimplePeak for the theoretical spectrum and its charges. Does not consider intensities.

Parameters

  alignment | The empty alignment, that will be filled by the algorithm
  fragment_mass_tolerance | The peak mass tolerance
  fragment_mass_tolerance_unit_ppm | True if the given tolerance is a ppm tolerance, false if tolerance is in Da
  theo_spectrum | The first spectrum to be aligned (preferably the theoretical one)
  exp_spectrum | the second spectrum to be aligned (preferably the experimental one)
  theo_charges | IntegerDataArray with charges for the theo_spectrum
  exp_charges | IntegerDataArray with charges for the exp_spectrum
  ppm_error_array | empty FloatDataArray to be filled with per peak ppm errors
  intensity_cutoff | Peaks will only be aligned if intensity1 / intensity2 > intensity_cutoff, with intensity1 being the lower of the two compared peaks and intensity2 the higher one. Set to 0 to ignore intensity differences.

## ◆ mergeAnnotatedSpectra()

static PeakSpectrum mergeAnnotatedSpectra | ( | PeakSpectrum & | first_spectrum,
|  | PeakSpectrum & | second_spectrum
| ) |  |

static

Merges two spectra into one while correctly considering metainfo in DataArrays.

Parameters

  first_spectrum |
  second_spectrum |

Returns
  A PeakSpectrum containing all peaks from both input spectra

## ◆ preprocessSpectra()

static PeakMap preprocessSpectra | ( | PeakMap & | exp,
|  | double | fragment_mass_tolerance,
|  | bool | fragment_mass_tolerance_unit_ppm,
|  | Size | peptide_min_size,
|  | Int | min_precursor_charge,
|  | Int | max_precursor_charge,
|  | bool | deisotope,
|  | bool | labeled
| ) |  |

static

Preprocesses spectra.

Filters out spectra with too few peaks (based on peptide_min_size) and those that do not fit into the precursor charge range. Removes zero intensity peaks and normalizes intensities. If the given tolerance is low enough, deisotoping is performed. Otherwise only the 500 most intense peaks are kept, if the param labeled is false. The number of returned spectra is equal to the number of input spectra for labeled data (otherwise not necessarily).

Parameters

  exp |
  fragment_mass_tolerance_xlinks |
  fragment_mass_tolerance_unit_ppm |
  peptide_min_size |
  min_precursor_charge |
  max_precursor_charge |
  labeled |

Returns
  A PeakMap of preprocessed spectra