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)
exp_charges	IntegerDataArray with charges for the exp_spectrum

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 from all spectra in exp. MS2 spectra are reduced in peak count using a WindowMower, if labeled is false. The number of returned spectra (MS2 only) is equal to the number of input MS2 spectra for labeled data (otherwise not necessarily).

Parameters

exp	Input data, which contains MS1 and MS2 spectra. Will be modified.
fragment_mass_tolerance	For deisotoping (used only if deisotope is true)
fragment_mass_tolerance_unit_ppm	For deisotoping (used only if deisotope is true)
peptide_min_size	Minimum length of a peptide (used to filter spectra with few peaks)
min_precursor_charge	MS2 spectra's minimal PC charge (ignored if labeled is true)
max_precursor_charge	MS2 spectra's maximal PC charge (ignored if labeled is true)
deisotope	Deisotope MS2 spectra?
labeled	Is the data labeled? (i.e. keep all MS2 spectra irrespective of precursor)

Returns

A PeakMap of preprocessed spectra (MS2 spectra only)