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 PeakSpectrum	deisotopeAndSingleChargeMSSpectrum (PeakSpectrum &old_spectrum, Int min_charge, Int max_charge, double fragment_tolerance, bool fragment_tolerance_unit_ppm, bool keep_only_deisotoped=false, Size min_isopeaks=3, Size max_isopeaks=10, bool make_single_charged=false)
	Deisotopes a spectrum and stores the determined charges in an IntegerDataArray. More...

Member Function Documentation

deisotopeAndSingleChargeMSSpectrum()

static PeakSpectrum deisotopeAndSingleChargeMSSpectrum ( PeakSpectrum &  old_spectrum, Int  min_charge, Int  max_charge, double  fragment_tolerance, bool  fragment_tolerance_unit_ppm, bool  keep_only_deisotoped = false, Size  min_isopeaks = 3, Size  max_isopeaks = 10, bool  make_single_charged = false  )

static

Deisotopes a spectrum and stores the determined charges in an IntegerDataArray.

If keep_only_deisotoped is false, the peaks that could not be deisotoped are assigned the charge 0. If an isotopic pattern contains more peaks than max_isopeaks, the rest are ignored for the current pattern.

Parameters

old_spectrum	The spectrum to be deisotoped
min_charge	Minimal charge to consider for the isotope patterns
max_charge	Maximal charge to consider for the isotope patterns
fragment_tolerance	The mass tolerance for matching peaks of an isotope pattern
fragment_tolerance_unit_ppm	True, if the given tolerance is in ppm, false if it is in Da
keep_only_deisotoped	True if the peaks that could not be deisotoped should be discarded
min_isopeaks	The minimal number of consecutive peaks in an isotopic pattern, before it gets acknowledged as an isotopic pattern
max_isopeaks	The maximal number of consecutive peaks in an isotopic pattern.
make_single_charged	If true, all peaks with charges larger than 1 are replaced with peaks with their corresponding single charged MZ

Returns

A PeakSpectrum annotated with charges

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.

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