OpenMS  2.4.0
PScore.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Timo Sachsenberg $
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34 
35 #pragma once
36 
38 
39 #include <OpenMS/CONCEPT/Types.h>
40 #include <vector>
41 #include <map>
42 
43 namespace OpenMS
44 {
49 struct OPENMS_DLLAPI PScore
50 {
51  /* @brief calculate local (windowed) peak ranks.
52  * The peak rank is defined as the number of neighboring peaks in +/- (mz_window/2) that have higher intensity
53  * The result can be used to efficiently filter spectra for top 1..n peaks in mass windows
54  * @note: ranks are zero based (highest intensity peak in window has rank 0)
55  * @param mz m/z positions of the peaks
56  * @param intensities of the peaks
57  * @param mz_window window in Thomson centered at each peak
58  */
59  static std::vector<Size> calculateIntensityRankInMZWindow(const std::vector<double>& mz, const std::vector<double>& intensities, double mz_window);
60 
61  /* @brief precalculated, windowed peak ranks for a whole experiment.
62  * The peak rank is defined as the number of neighboring peaks in +/- (mz_window/2) that have higher intensity
63  * 1. Each spectrum is subdivided into windows of size @param mz_window.
64  * 2. For each window, peak ranks are assigned using calculateIntensityRankInMZWindow.
65  * 3. A rank map is returned
66  * @note: ranks are zero based (top element has rank 0)
67  * @param peak_map Fragment spectra used for rank calculation. Typically a peak map after removal of all MS1 spectra.
68  * @param mz_window window in Thomson centered at each peak
69  */
70  static std::vector<std::vector<Size> > calculateRankMap(const PeakMap& peak_map, double mz_window = 100);
71 
72  /* @brief Calculates spectra for peak level between min_level to max_level and stores them in the map
73  * A spectrum of peak level n retains the (n+1) top intensity peaks in a sliding mz_window centered at each peak.
74  * @note: levels are zero based (level 0 has only the top intensity peaks for each window, level 1 the top and second most intensive one)
75  * @note: min and max level are taken from the Andromeda publication but are similar to the AScore publication
76  */
77  static std::map<Size, PeakSpectrum > calculatePeakLevelSpectra(const PeakSpectrum& spec, const std::vector<Size>& ranks, Size min_level = 1, Size max_level = 9);
78 
79  /* @brief Computes the PScore for a vector of theoretical spectra
80  * Similar to Andromeda, a vector of theoretical spectra can be provided that e.g. contain loss spectra or higher charge spectra depending on the sequence.
81  * The best score obtained by scoring all those theoretical spectra against the experimental ones is returned.
82  * @param fragment_mass_tolerance mass tolerance for matching peaks
83  * @param fragment_mass_tolerance_unit_ppm whether Thomson or ppm is used
84  * @param peak_level_spectra spectra for different peak levels (=filtered by maximum rank).
85  * @param theo_spectra theoretical spectra as obtained e.g. from TheoreticalSpectrumGenerator
86  * @param mz_window window in Thomson centered at each peak
87  */
88  static double computePScore(double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const std::map<Size, PeakSpectrum>& peak_level_spectra, const std::vector<PeakSpectrum>& theo_spectra, double mz_window = 100.0);
89 
90  /* @brief Computes the PScore for a single theoretical spectrum
91  * @param fragment_mass_tolerance mass tolerance for matching peaks
92  * @param fragment_mass_tolerance_unit_ppm whether Thomson or ppm is used
93  * @param peak_level_spectra spectra for different peak levels (=filtered by maximum rank).
94  * @param theo_spectra theoretical spectra as obtained e.g. from TheoreticalSpectrumGenerator
95  * @param mz_window window in Thomson centered at each peak
96  */
97  static double computePScore(double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const std::map<Size, PeakSpectrum>& peak_level_spectra, const PeakSpectrum& theo_spectrum, double mz_window = 100.0);
98 
101  static double massCorrectionTerm(double mass);
102 
105  static double cleavageCorrectionTerm(Size cleavages, bool consecutive_cleavage);
106 
109  static double modificationCorrectionTerm(Size modifications);
110 };
111 
112 }
113 
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
Implementation of the PScore PSM scoring algorithm.
Definition: PScore.h:49
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127