PrecursorPurity.h

Go to the documentation of this file.

// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Eugen Netz $
// $Authors: Eugen Netz $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <unordered_map>
#include <vector>
 
 
namespace OpenMS
{
  class AASequence;
 
  class OPENMS_DLLAPI PrecursorPurity
  {
 
  public:
 
    struct PurityScores
    {
      double total_intensity = 0.0;
      double target_intensity = 0.0;
      double signal_proportion = 0.0;
      Size target_peak_count = 0;
      Size interfering_peak_count = 0;
      PeakSpectrum interfering_peaks; // peaks left after precursor (isotopic) peaks have been removed
    };
 
    static std::unordered_map<std::string, PurityScores> computePrecursorPurities(const PeakMap& spectra, double precursor_mass_tolerance, bool precursor_mass_tolerance_unit_ppm, bool ignore_missing_precursor_spectra = false);
 
    static PurityScores computePrecursorPurity(const PeakSpectrum& ms1, const Precursor& pre, const double precursor_mass_tolerance, const bool precursor_mass_tolerance_unit_ppm);
 
    static std::vector<double> computeSingleScanPrecursorPurities(int ms2_spec_idx, int precursor_spec_idx, const MSExperiment & exp, double max_precursor_isotope_deviation);
    
    static std::vector<double> computeInterpolatedPrecursorPurity(int ms2_spec_idx, int precursor_spec_idx, int next_ms1_spec_idx, const MSExperiment & exp, double max_precursor_isotope_deviation);
 
    static Size countSPSPrecursorsMatchingPeptideFragments(const std::vector<Precursor>& sps_precursors, const AASequence& peptide, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, int max_fragment_charge = 1);
 
  private:
    // simple helper to combine the metrics contained in two PurityScores
    static PurityScores combinePrecursorPurities(const PrecursorPurity::PurityScores& score1, const PrecursorPurity::PurityScores& score2);
 
  };
}