#include <OpenMS/ANALYSIS/XLMS/OPXLSpectrumProcessingAlgorithms.h>
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static PeakSpectrum | mergeAnnotatedSpectra (PeakSpectrum &first_spectrum, PeakSpectrum &second_spectrum) |
| Merges two spectra into one while correctly considering metainfo in DataArrays. More...
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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...
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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...
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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...
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◆ getSpectrumAlignmentFastCharge()
Computes a spectrum alignment while considering fragment charges stored in a IntegerDataArray and a cut-off for the intensity difference ratio.
- Parameters
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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()
Computes a spectrum alignment while considering fragment charges. Uses TSGXLMS::SimplePeak for the theoretical spectrum and its charges. Does not consider intensities.
- Parameters
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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()
Merges two spectra into one while correctly considering metainfo in DataArrays.
- Parameters
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first_spectrum | |
second_spectrum | |
- Returns
- A PeakSpectrum containing all peaks from both input spectra
◆ preprocessSpectra()
static PeakMap preprocessSpectra |
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PeakMap & |
exp, |
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double |
fragment_mass_tolerance, |
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bool |
fragment_mass_tolerance_unit_ppm, |
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Size |
peptide_min_size, |
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Int |
min_precursor_charge, |
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Int |
max_precursor_charge, |
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bool |
deisotope, |
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bool |
labeled |
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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
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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)