#include <psmfeatures.h>

Public Member Functions
	PsmFeatures (PrecisionPtr ms2precision, double minimumMz)
	compute psm features More...

	~PsmFeatures ()

void	setPeptideSpectrumCharge (const pappso::PeptideSp peptideSp, const MassSpectrum *p_spectrum, unsigned int parent_charge)

double	getIntensityOfMatchedIon (PeptideIon ion_type)
	get the sum of intensity of a specific ion More...

double	getTotalIntensity () const
	sum of all peak intensities (matched or not) More...

double	getTotalIntensityOfMatchedIons () const
	sum of matched peak intensities More...

std::size_t	getNumberOfMatchedIons () const
	number of matched ions (peaks) More...

std::size_t	countMatchedIonComplementPairs () const
	count the number of matched ion complement More...

double	getTotalIntensityOfMatchedIonComplementPairs () const
	intensity of matched ion complement More...

const std::vector< std::pair< pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch > > &	getPeakIonPairs () const

double	getMatchedMzDiffMean () const
	get mean deviation of matched peak mass delta More...

double	getMatchedMzDiffSd () const
	get standard deviation of matched peak mass delta More...

double	getMaxIntensityMatchedIonComplementPairPrecursorMassDelta () const
	get the precursor mass delta of the maximum intensity pair of complement ions More...

std::size_t	getMaxConsecutiveIon (PeptideIon ion_type)
	get the maximum consecutive fragments of one ion type More...

std::size_t	getAaSequenceCoverage (PeptideIon ion_type)
	number of amino acid covered by matched ions More...

std::size_t	getComplementPairsAaSequenceCoverage ()
	number of amino acid covered by matched complement pairs of ions More...

double	getMaxIntensityPeakIonMatch (PeptideIon ion_type) const

double	getIonPairPrecursorMassDelta (const std::pair< pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch > &ion_pair) const

Private Member Functions
void	findComplementIonPairs (const pappso::PeptideSp &peptideSp)

Private Attributes
std::shared_ptr< FilterChargeDeconvolution >	msp_filterChargeDeconvolution

std::shared_ptr< FilterMzExclusion >	msp_filterMzExclusion

std::shared_ptr< FilterResampleKeepGreater >	msp_filterKeepGreater

std::shared_ptr< PeptideIsotopeSpectrumMatch >	msp_peptideSpectrumMatch

pappso::PeptideSp	msp_peptide

PrecisionPtr	m_ms2precision

std::list< PeptideIon >	m_ionList

double	m_spectrumSumIntensity

double	m_precursorTheoreticalMz

double	m_precursorTheoreticalMass

unsigned int	m_parentCharge = 1

std::vector< std::pair< pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch > >	m_peakIonPairs

double	m_matchedMzDiffMean = 0

double	m_matchedMzDiffMedian = 0

double	m_matchedMzDiffSd = 0

Detailed Description

Todo:: write docs

Definition at line 43 of file psmfeatures.h.

Constructor & Destructor Documentation

◆ PsmFeatures()

PsmFeatures::PsmFeatures	(	PrecisionPtr	ms2precision,
		double	minimumMz
	)

compute psm features

Parameters

ms2precision	precision of mass measurements for MS2 fragments
minimumMz	ignore mz values under this threshold

Definition at line 35 of file psmfeatures.cpp.

{
 
  m_ms2precision = ms2precision;
 
  m_ionList.push_back(PeptideIon::y);
  m_ionList.push_back(PeptideIon::b);
 
 
  msp_filterKeepGreater =
    std::make_shared<FilterResampleKeepGreater>(minimumMz);
 
  msp_filterChargeDeconvolution =
    std::make_shared<FilterChargeDeconvolution>(m_ms2precision);
  msp_filterMzExclusion = std::make_shared<FilterMzExclusion>(
    PrecisionFactory::getPrecisionPtrFractionInstance(m_ms2precision, 0.5));
}

References pappso::b, pappso::PrecisionFactory::getPrecisionPtrFractionInstance(), m_ionList, m_ms2precision, msp_filterChargeDeconvolution, msp_filterKeepGreater, msp_filterMzExclusion, and pappso::y.

◆ ~PsmFeatures()

PsmFeatures::~PsmFeatures ( )

Destructor

Definition at line 53 of file psmfeatures.cpp.

54{

55}

Member Function Documentation

◆ countMatchedIonComplementPairs()

std::size_t pappso::PsmFeatures::countMatchedIonComplementPairs ( ) const

count the number of matched ion complement

matched ion complement are ions with a sum compatible to the precursor mass

Definition at line 166 of file psmfeatures.cpp.

{
  return m_peakIonPairs.size();
}

◆ findComplementIonPairs()

void pappso::PsmFeatures::findComplementIonPairs ( const pappso::PeptideSp & peptideSp )

private

Definition at line 366 of file psmfeatures.cpp.

{
  std::size_t peptide_size = peptideSp.get()->size();
  std::vector<PeakIonIsotopeMatch> ion_isotope_list(
    msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList().begin(),
    msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList().end());
  for(const pappso::PeakIonIsotopeMatch &peak_ion_ext : ion_isotope_list)
    {
      if(peptideIonIsNter(peak_ion_ext.getPeptideIonType()))
        {
          auto it = findComplementIonType(ion_isotope_list.begin(),
                                          ion_isotope_list.end(),
                                          peak_ion_ext,
                                          peptide_size);
          if(it != ion_isotope_list.end())
            { // contains the complementary ion
              m_peakIonPairs.push_back({peak_ion_ext, *it});
            }
        }
    }
}

References pappso::findComplementIonType(), and pappso::peptideIonIsNter().

Referenced by setPeptideSpectrumCharge().

◆ getAaSequenceCoverage()

std::size_t pappso::PsmFeatures::getAaSequenceCoverage ( pappso::PeptideIon ion_type )

number of amino acid covered by matched ions

Definition at line 269 of file psmfeatures.cpp.

{
  std::vector<bool> covered;
  covered.resize(msp_peptide.get()->size(), false);
 
  for(auto &peak : msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList())
    {
      if(peak.getPeptideIonType() == ion_type)
        {
          covered[peak.getPeptideFragmentIonSp().get()->size() - 1] = true;
        }
    }
  return std::count(covered.begin(), covered.end(), true);
}

◆ getComplementPairsAaSequenceCoverage()

std::size_t pappso::PsmFeatures::getComplementPairsAaSequenceCoverage ( )

number of amino acid covered by matched complement pairs of ions

Definition at line 285 of file psmfeatures.cpp.

{
 
  std::vector<bool> covered;
  covered.resize(msp_peptide.get()->size(), false);
 
  for(auto &peak_pair : m_peakIonPairs)
    {
      std::size_t pos =
        peak_pair.first.getPeptideFragmentIonSp().get()->size() - 1;
      covered[pos]     = true;
      covered[pos + 1] = true;
    }
  return std::count(covered.begin(), covered.end(), true);
}

◆ getIntensityOfMatchedIon()

double PsmFeatures::getIntensityOfMatchedIon ( PeptideIon ion_type )

get the sum of intensity of a specific ion

Parameters

ion_type ion species (y, b, ...)

Definition at line 136 of file psmfeatures.cpp.

{
  double sum = 0;
  for(const PeakIonMatch &peak_ion_match : *msp_peptideSpectrumMatch.get())
    {
      if(peak_ion_match.getPeptideIonType() == ion_type)
        {
          sum += peak_ion_match.getPeak().y;
        }
    }
  return sum;
}

References msp_peptideSpectrumMatch, and pappso::sum.

◆ getIonPairPrecursorMassDelta()

double pappso::PsmFeatures::getIonPairPrecursorMassDelta ( const std::pair< pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch > & ion_pair ) const

Definition at line 346 of file psmfeatures.cpp.

{
  qDebug() << m_precursorTheoreticalMz << " " << ion_pair.first.getPeak().x
           << " " << ion_pair.second.getPeak().x << " "
           << ion_pair.second.getCharge() << " " << ion_pair.first.getCharge()
           << " " << m_parentCharge;
  double diff =
    (m_precursorTheoreticalMass + (MHPLUS * ion_pair.first.getCharge())) /
    ion_pair.first.getCharge();
 
 
  return (diff - (ion_pair.first.getPeak().x + ion_pair.second.getPeak().x -
                  ((MHPLUS * ion_pair.first.getCharge())) /
                    ion_pair.first.getCharge()));
}

References pappso::MHPLUS().

◆ getMatchedMzDiffMean()

double pappso::PsmFeatures::getMatchedMzDiffMean ( ) const

get mean deviation of matched peak mass delta

Definition at line 198 of file psmfeatures.cpp.

{
  return m_matchedMzDiffMean;
}

◆ getMatchedMzDiffSd()

double pappso::PsmFeatures::getMatchedMzDiffSd ( ) const

get standard deviation of matched peak mass delta

Definition at line 192 of file psmfeatures.cpp.

{
  return m_matchedMzDiffSd;
}

◆ getMaxConsecutiveIon()

std::size_t pappso::PsmFeatures::getMaxConsecutiveIon ( pappso::PeptideIon ion_type )

get the maximum consecutive fragments of one ion type

Parameters

ion_type ion species (y, b, ...)

Definition at line 211 of file psmfeatures.cpp.

{
  std::size_t max = 0;
  auto peak_ion_match_list =
    msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList();
 
  peak_ion_match_list.erase(
    std::remove_if(
      peak_ion_match_list.begin(),
      peak_ion_match_list.end(),
      [ion_type](const PeakIonIsotopeMatch &a) {
        if(a.getPeptideIonType() != ion_type)
          return true;
        if(a.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber() > 0)
          return true;
        return false;
      }),
    peak_ion_match_list.end());
 
  peak_ion_match_list.sort(
    [](const PeakIonIsotopeMatch &a, const PeakIonIsotopeMatch &b) {
      if(a.getCharge() < b.getCharge())
        return true;
      if(a.getPeptideIonType() < b.getPeptideIonType())
        return true;
      if(a.getPeptideFragmentIonSp().get()->size() <
         b.getPeptideFragmentIonSp().get()->size())
        return true;
      return false;
    });
 
  unsigned int charge = 0;
  std::size_t size    = 0;
  std::size_t count   = 0;
  for(std::list<PeakIonIsotopeMatch>::iterator it = peak_ion_match_list.begin();
      it != peak_ion_match_list.end();
      it++)
    {
      qDebug()
        << it->toString() << max << " " << it->getPeak().x << " "
        << it->getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber();
      count++;
      if((charge != it->getCharge()) ||
         (size != (it->getPeptideFragmentIonSp().get()->size() - 1)))
        {
          count  = 1;
          charge = it->getCharge();
        }
      if(max < count)
        max = count;
 
      size = it->getPeptideFragmentIonSp().get()->size();
    }
 
  return max;
}

References pappso::a, pappso::b, and pappso::max.

◆ getMaxIntensityMatchedIonComplementPairPrecursorMassDelta()

double pappso::PsmFeatures::getMaxIntensityMatchedIonComplementPairPrecursorMassDelta ( ) const

get the precursor mass delta of the maximum intensity pair of complement ions

Definition at line 325 of file psmfeatures.cpp.

{
  auto peak_it = std::max_element(
    m_peakIonPairs.begin(),
    m_peakIonPairs.end(),
    [](const std::pair<pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch>
         &a,
       const std::pair<pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch>
         &b) {
      return ((a.first.getPeak().y + a.second.getPeak().y) <
              (b.first.getPeak().y + b.second.getPeak().y));
    });
 
  if(peak_it == m_peakIonPairs.end())
    return 0;
 
  return getIonPairPrecursorMassDelta(*peak_it);
}

References pappso::a, and pappso::b.

◆ getMaxIntensityPeakIonMatch()

double pappso::PsmFeatures::getMaxIntensityPeakIonMatch ( pappso::PeptideIon ion_type ) const

Definition at line 303 of file psmfeatures.cpp.

{
  std::list<pappso::PeakIonIsotopeMatch> peak_ion_type =
    msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList();
 
  peak_ion_type.remove_if([ion_type](const PeakIonIsotopeMatch &a) {
    return (a.getPeptideIonType() != ion_type);
  });
  auto peak_it = std::max_element(
    peak_ion_type.begin(),
    peak_ion_type.end(),
    [](const PeakIonIsotopeMatch &a, const PeakIonIsotopeMatch &b) {
      return (a.getPeak().y < b.getPeak().y);
    });
 
  if(peak_it == peak_ion_type.end())
    return 0;
  return peak_it->getPeak().y;
}

References pappso::a, and pappso::b.

◆ getNumberOfMatchedIons()

std::size_t pappso::PsmFeatures::getNumberOfMatchedIons ( ) const

number of matched ions (peaks)

Definition at line 205 of file psmfeatures.cpp.

{
  return msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList().size();
}

◆ getPeakIonPairs()

const std::vector< std::pair< pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch > > & pappso::PsmFeatures::getPeakIonPairs ( ) const

Definition at line 173 of file psmfeatures.cpp.

{
  return m_peakIonPairs;
}

◆ getTotalIntensity()

double PsmFeatures::getTotalIntensity ( ) const

sum of all peak intensities (matched or not)

Definition at line 160 of file psmfeatures.cpp.

{
  return m_spectrumSumIntensity;
}

References m_spectrumSumIntensity.

◆ getTotalIntensityOfMatchedIonComplementPairs()

double pappso::PsmFeatures::getTotalIntensityOfMatchedIonComplementPairs ( ) const

intensity of matched ion complement

Definition at line 179 of file psmfeatures.cpp.

{
 
  double sum = 0;
  for(auto &peak_pairs : m_peakIonPairs)
    {
      sum += peak_pairs.first.getPeak().y;
      sum += peak_pairs.second.getPeak().y;
    }
  return sum;
}

References pappso::sum.

◆ getTotalIntensityOfMatchedIons()

double PsmFeatures::getTotalIntensityOfMatchedIons ( ) const

sum of matched peak intensities

Definition at line 149 of file psmfeatures.cpp.

{
  double sum = 0;
  for(const PeakIonMatch &peak_ion_match : *msp_peptideSpectrumMatch.get())
    {
      sum += peak_ion_match.getPeak().y;
    }
  return sum;
}

References msp_peptideSpectrumMatch, and pappso::sum.

◆ setPeptideSpectrumCharge()

void PsmFeatures::setPeptideSpectrumCharge	(	const pappso::PeptideSp	peptideSp,
		const MassSpectrum *	p_spectrum,
		unsigned int	parent_charge
	)

Definition at line 58 of file psmfeatures.cpp.

{
  m_peakIonPairs.clear();
  msp_peptide = peptideSp;
  MassSpectrum spectrum(*p_spectrum);
  msp_filterKeepGreater.get()->filter(spectrum);
  // msp_filterChargeDeconvolution.get()->filter(spectrum);
  // msp_filterMzExclusion.get()->filter(spectrum);
 
  msp_peptideSpectrumMatch =
    std::make_shared<PeptideIsotopeSpectrumMatch>(spectrum,
                                                  peptideSp,
                                                  parent_charge,
                                                  m_ms2precision,
                                                  m_ionList,
                                                  (unsigned int)1,
                                                  0);
 
  msp_peptideSpectrumMatch.get()->dropPeaksLackingMonoisotope();
  m_spectrumSumIntensity = spectrum.sumY();
 
 
  qDebug() << " accumulate";
  std::vector<double> delta_list;
 
 
  // TODO compute number of matched complementary peaks having m/z compatible
  // with the precursor
 
  m_precursorTheoreticalMz   = peptideSp.get()->getMz(parent_charge);
  m_precursorTheoreticalMass = peptideSp.get()->getMass();
  m_parentCharge             = parent_charge;
 
 
  findComplementIonPairs(peptideSp);
 
 
  for(const pappso::PeakIonIsotopeMatch &peak_ion :
      msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList())
    {
      delta_list.push_back(
        peak_ion.getPeptideFragmentIonSp().get()->getMz(peak_ion.getCharge()) -
        peak_ion.getPeak().x);
    }
  pappso::pappso_double sum =
    std::accumulate(delta_list.begin(), delta_list.end(), 0);
 
  qDebug() << " delta_list.size()=" << delta_list.size();
  m_matchedMzDiffMean   = 0;
  m_matchedMzDiffMedian = 0;
  m_matchedMzDiffSd     = 0;
  if(delta_list.size() > 0)
    {
      m_matchedMzDiffMean = sum / ((pappso::pappso_double)delta_list.size());
 
      std::sort(delta_list.begin(), delta_list.end());
      m_matchedMzDiffMedian = delta_list[(delta_list.size() / 2)];
 
 
      qDebug() << " sd";
      m_matchedMzDiffSd = 0;
      for(pappso::pappso_double val : delta_list)
        {
          // sd = sd + ((val - mean) * (val - mean));
          m_matchedMzDiffSd += std::pow((val - m_matchedMzDiffMean), 2);
        }
      m_matchedMzDiffSd = m_matchedMzDiffSd / delta_list.size();
      m_matchedMzDiffSd = std::sqrt(m_matchedMzDiffSd);
    }
  else
    {
    }
}

References findComplementIonPairs(), m_ionList, m_matchedMzDiffMean, m_matchedMzDiffMedian, m_matchedMzDiffSd, m_ms2precision, m_parentCharge, m_peakIonPairs, m_precursorTheoreticalMass, m_precursorTheoreticalMz, m_spectrumSumIntensity, msp_filterKeepGreater, msp_peptide, msp_peptideSpectrumMatch, pappso::sum, and pappso::Trace::sumY().

Member Data Documentation

◆ m_ionList

std::list<PeptideIon> pappso::PsmFeatures::m_ionList

private

Definition at line 145 of file psmfeatures.h.

Referenced by PsmFeatures(), and setPeptideSpectrumCharge().

◆ m_matchedMzDiffMean

double pappso::PsmFeatures::m_matchedMzDiffMean = 0

private

Definition at line 157 of file psmfeatures.h.

Referenced by setPeptideSpectrumCharge().

◆ m_matchedMzDiffMedian

double pappso::PsmFeatures::m_matchedMzDiffMedian = 0

private

Definition at line 158 of file psmfeatures.h.

Referenced by setPeptideSpectrumCharge().

◆ m_matchedMzDiffSd

double pappso::PsmFeatures::m_matchedMzDiffSd = 0

private

Definition at line 159 of file psmfeatures.h.

Referenced by setPeptideSpectrumCharge().

◆ m_ms2precision

PrecisionPtr pappso::PsmFeatures::m_ms2precision

private

Definition at line 144 of file psmfeatures.h.

Referenced by PsmFeatures(), and setPeptideSpectrumCharge().

◆ m_parentCharge

unsigned int pappso::PsmFeatures::m_parentCharge = 1

private

Definition at line 151 of file psmfeatures.h.

Referenced by setPeptideSpectrumCharge().

◆ m_peakIonPairs

std::vector< std::pair<pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch> > pappso::PsmFeatures::m_peakIonPairs

private

Definition at line 155 of file psmfeatures.h.

Referenced by setPeptideSpectrumCharge().

◆ m_precursorTheoreticalMass

double pappso::PsmFeatures::m_precursorTheoreticalMass

private

Definition at line 150 of file psmfeatures.h.

Referenced by setPeptideSpectrumCharge().

◆ m_precursorTheoreticalMz

double pappso::PsmFeatures::m_precursorTheoreticalMz

private

Definition at line 149 of file psmfeatures.h.

Referenced by setPeptideSpectrumCharge().

◆ m_spectrumSumIntensity

double pappso::PsmFeatures::m_spectrumSumIntensity

private

Definition at line 147 of file psmfeatures.h.

Referenced by getTotalIntensity(), and setPeptideSpectrumCharge().

◆ msp_filterChargeDeconvolution

std::shared_ptr<FilterChargeDeconvolution> pappso::PsmFeatures::msp_filterChargeDeconvolution

private

Definition at line 137 of file psmfeatures.h.

Referenced by PsmFeatures().

◆ msp_filterKeepGreater

std::shared_ptr<FilterResampleKeepGreater> pappso::PsmFeatures::msp_filterKeepGreater

private

Definition at line 139 of file psmfeatures.h.

Referenced by PsmFeatures(), and setPeptideSpectrumCharge().

◆ msp_filterMzExclusion

std::shared_ptr<FilterMzExclusion> pappso::PsmFeatures::msp_filterMzExclusion

private

Definition at line 138 of file psmfeatures.h.

Referenced by PsmFeatures().

◆ msp_peptide

pappso::PeptideSp pappso::PsmFeatures::msp_peptide

private

Definition at line 142 of file psmfeatures.h.

Referenced by setPeptideSpectrumCharge().

◆ msp_peptideSpectrumMatch

std::shared_ptr<PeptideIsotopeSpectrumMatch> pappso::PsmFeatures::msp_peptideSpectrumMatch

private

Definition at line 141 of file psmfeatures.h.

Referenced by getIntensityOfMatchedIon(), getTotalIntensityOfMatchedIons(), and setPeptideSpectrumCharge().

The documentation for this class was generated from the following files:

pappsomspp/psm/features/psmfeatures.h
pappsomspp/psm/features/psmfeatures.cpp

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PsmFeatures()

◆ ~PsmFeatures()

Member Function Documentation

◆ countMatchedIonComplementPairs()

◆ findComplementIonPairs()

◆ getAaSequenceCoverage()

◆ getComplementPairsAaSequenceCoverage()

◆ getIntensityOfMatchedIon()

◆ getIonPairPrecursorMassDelta()

◆ getMatchedMzDiffMean()

◆ getMatchedMzDiffSd()

◆ getMaxConsecutiveIon()

◆ getMaxIntensityMatchedIonComplementPairPrecursorMassDelta()

◆ getMaxIntensityPeakIonMatch()

◆ getNumberOfMatchedIons()

◆ getPeakIonPairs()

◆ getTotalIntensity()

◆ getTotalIntensityOfMatchedIonComplementPairs()

◆ getTotalIntensityOfMatchedIons()

◆ setPeptideSpectrumCharge()

Member Data Documentation

◆ m_ionList

◆ m_matchedMzDiffMean

◆ m_matchedMzDiffMedian

◆ m_matchedMzDiffSd

◆ m_ms2precision

◆ m_parentCharge

◆ m_peakIonPairs

◆ m_precursorTheoreticalMass

◆ m_precursorTheoreticalMz

◆ m_spectrumSumIntensity

◆ msp_filterChargeDeconvolution

◆ msp_filterKeepGreater

◆ msp_filterMzExclusion

◆ msp_peptide

◆ msp_peptideSpectrumMatch