#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_xlinks, bool fragment_mass_tolerance_unit_ppm, Size peptide_min_size, Int min_precursor_charge, Int max_precursor_charge, bool labeled) |
| | Preprocesses spectra. More...
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| static void | getSpectrumAlignment (std::vector< std::pair< Size, Size > > &alignment, const PeakSpectrum &s1, const PeakSpectrum &s2, double tolerance, bool relative_tolerance, double intensity_cutoff=0.0) |
| | Computes a spectrum alignment while considering fragment charges stored in a IntegerDataArray and an intensity difference ratio. More...
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| 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...
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◆ deisotopeAndSingleChargeMSSpectrum()
| static PeakSpectrum deisotopeAndSingleChargeMSSpectrum |
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PeakSpectrum & |
old_spectrum, |
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Int |
min_charge, |
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Int |
max_charge, |
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double |
fragment_tolerance, |
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bool |
fragment_tolerance_unit_ppm, |
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bool |
keep_only_deisotoped = false, |
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Size |
min_isopeaks = 3, |
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Size |
max_isopeaks = 10, |
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bool |
make_single_charged = false |
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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
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| 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
◆ getSpectrumAlignment()
Computes a spectrum alignment while considering fragment charges stored in a IntegerDataArray and an intensity difference ratio.
- Parameters
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| alignment | The empty alignment, that will be filled by the algorithm |
| s1 | The first spectrum to be aligned |
| s2 | the second spectrum to be aligned |
| tolerance | The peak mass tolerance |
| relative_tolerance | True if the given tolerance is a ppm tolerance, false if tolerance is in Da |
| 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()
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_xlinks, |
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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 |
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. 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
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| 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