libpappsomspp
Library for mass spectrometry
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pappso::PsmFeatures Class Reference

#include <psmfeatures.h>

Public Member Functions

 PsmFeatures (PrecisionPtr ms2precision, double minimumMz)
 compute psm features
 
 ~PsmFeatures ()
 
void setPeptideSpectrumCharge (const pappso::PeptideSp peptideSp, const MassSpectrum *p_spectrum, unsigned int parent_charge, unsigned int max_isotope_number)
 
double getIntensityOfMatchedIon (PeptideIon ion_type)
 get the sum of intensity of a specific ion
 
double getTotalIntensity () const
 sum of all peak intensities (matched or not)
 
double getTotalIntensityOfMatchedIons () const
 sum of matched peak intensities
 
std::size_t getNumberOfMatchedIons () const
 number of matched ions (peaks)
 
std::size_t countMatchedIonComplementPairs () const
 count the number of matched ion complement
 
double getTotalIntensityOfMatchedIonComplementPairs () const
 intensity of matched ion complement
 
const std::vector< std::pair< pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch > > & getPeakIonPairs () const
 
double getMatchedMzDiffMean () const
 get mean deviation of matched peak mass delta
 
double getMatchedMzDiffSd () const
 get standard deviation of matched peak mass delta
 
double getMaxIntensityMatchedIonComplementPairPrecursorMassDelta () const
 get the precursor mass delta of the maximum intensity pair of complement ions
 
std::size_t getMaxConsecutiveIon (PeptideIon ion_type)
 get the maximum consecutive fragments of one ion type
 
std::size_t getAaSequenceCoverage (PeptideIon ion_type)
 number of amino acid covered by matched ions
 
std::size_t getComplementPairsAaSequenceCoverage ()
 number of amino acid covered by matched complement pairs of ions
 
double getMaxIntensityPeakIonMatch (PeptideIon ion_type) const
 
double getIonPairPrecursorMassDelta (const std::pair< pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch > &ion_pair) const
 
LinearRegression getIonIsotopeLinearRegression () const
 

Private Member Functions

void findComplementIonPairs (const pappso::PeptideSp &peptideSp)
 

Private Attributes

std::shared_ptr< FilterChargeDeconvolutionmsp_filterChargeDeconvolution
 
std::shared_ptr< FilterMzExclusionmsp_filterMzExclusion
 
std::shared_ptr< FilterResampleKeepGreatermsp_filterKeepGreater
 
std::shared_ptr< PeptideIsotopeSpectrumMatchmsp_peptideSpectrumMatch
 
pappso::PeptideSp msp_peptide
 
PrecisionPtr m_ms2precision
 
std::list< PeptideIonm_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 45 of file psmfeatures.h.

Constructor & Destructor Documentation

◆ PsmFeatures()

PsmFeatures::PsmFeatures ( PrecisionPtr  ms2precision,
double  minimumMz 
)

compute psm features

Parameters
ms2precisionprecision of mass measurements for MS2 fragments
minimumMzignore mz values under this threshold

Definition at line 35 of file psmfeatures.cpp.

36{
37
38 m_ms2precision = ms2precision;
39
40 m_ionList.push_back(PeptideIon::y);
41 m_ionList.push_back(PeptideIon::b);
42
43
45 std::make_shared<FilterResampleKeepGreater>(minimumMz);
46
48 std::make_shared<FilterChargeDeconvolution>(m_ms2precision);
49 msp_filterMzExclusion = std::make_shared<FilterMzExclusion>(
51}
static PrecisionPtr getPrecisionPtrFractionInstance(PrecisionPtr origin, double fraction)
get the fraction of an existing precision pointer
std::shared_ptr< FilterChargeDeconvolution > msp_filterChargeDeconvolution
std::shared_ptr< FilterResampleKeepGreater > msp_filterKeepGreater
std::shared_ptr< FilterMzExclusion > msp_filterMzExclusion
std::list< PeptideIon > m_ionList
PrecisionPtr m_ms2precision
@ y
Cter amino ions.
@ b
Nter acylium ions.

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 167 of file psmfeatures.cpp.

168{
169 return m_peakIonPairs.size();
170}
std::vector< std::pair< pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch > > m_peakIonPairs

◆ findComplementIonPairs()

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

Definition at line 371 of file psmfeatures.cpp.

372{
373 std::size_t peptide_size = peptideSp.get()->size();
374 std::vector<PeakIonIsotopeMatch> ion_isotope_list(
375 msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList().begin(),
376 msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList().end());
377 for(const pappso::PeakIonIsotopeMatch &peak_ion_ext : ion_isotope_list)
378 {
379 if(peptideIonIsNter(peak_ion_ext.getPeptideIonType()))
380 {
381 auto it = findComplementIonType(ion_isotope_list.begin(),
382 ion_isotope_list.end(),
383 peak_ion_ext,
384 peptide_size);
385 if(it != ion_isotope_list.end())
386 { // contains the complementary ion
387 m_peakIonPairs.push_back({peak_ion_ext, *it});
388 }
389 }
390 }
391}
std::shared_ptr< PeptideIsotopeSpectrumMatch > msp_peptideSpectrumMatch
std::vector< PeakIonIsotopeMatch >::iterator findComplementIonType(std::vector< PeakIonIsotopeMatch >::iterator begin, std::vector< PeakIonIsotopeMatch >::iterator end, const PeakIonIsotopeMatch &peak_ion, std::size_t peptide_size)
find the first element containing the complementary ion complementary ion of y1 is b(n-1) for instanc...
bool peptideIonIsNter(PeptideIon ion_type)
tells if an ion is Nter
Definition peptide.cpp:60

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 270 of file psmfeatures.cpp.

271{
272 std::vector<bool> covered;
273 covered.resize(msp_peptide.get()->size(), false);
274
275 for(auto &peak : msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList())
276 {
277 if(peak.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber() ==
278 0)
279 { // only count with monotisotopic
280 if(peak.getPeptideIonType() == ion_type)
281 {
282 covered[peak.getPeptideFragmentIonSp().get()->size() - 1] = true;
283 }
284 }
285 }
286 return std::count(covered.begin(), covered.end(), true);
287}
pappso::PeptideSp msp_peptide

◆ getComplementPairsAaSequenceCoverage()

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

number of amino acid covered by matched complement pairs of ions

Definition at line 290 of file psmfeatures.cpp.

291{
292
293 std::vector<bool> covered;
294 covered.resize(msp_peptide.get()->size(), false);
295
296 for(auto &peak_pair : m_peakIonPairs)
297 {
298 std::size_t pos =
299 peak_pair.first.getPeptideFragmentIonSp().get()->size() - 1;
300 covered[pos] = true;
301 covered[pos + 1] = true;
302 }
303 return std::count(covered.begin(), covered.end(), true);
304}

◆ getIntensityOfMatchedIon()

double PsmFeatures::getIntensityOfMatchedIon ( PeptideIon  ion_type)

get the sum of intensity of a specific ion

Parameters
ion_typeion species (y, b, ...)

Definition at line 137 of file psmfeatures.cpp.

138{
139 double sum = 0;
140 for(const PeakIonMatch &peak_ion_match : *msp_peptideSpectrumMatch.get())
141 {
142 if(peak_ion_match.getPeptideIonType() == ion_type)
143 {
144 sum += peak_ion_match.getPeak().y;
145 }
146 }
147 return sum;
148}
@ sum
sum of intensities

References msp_peptideSpectrumMatch, and pappso::sum.

◆ getIonIsotopeLinearRegression()

LinearRegression pappso::PsmFeatures::getIonIsotopeLinearRegression ( ) const

experimental use with caution

Definition at line 395 of file psmfeatures.cpp.

396{
397 std::size_t peptide_size = msp_peptide.get()->size();
398 std::vector<PeakIonIsotopeMatch> ion_isotope_list(
399 msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList().begin(),
400 msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList().end());
401
402 Trace scaterplot;
403
404 for(PeptideIon ion_type : m_ionList)
405 {
406 std::vector<double> mono_th_intensities(peptide_size, 0);
407 std::vector<double> isotope_th_intensities(peptide_size, 0);
408
409 std::vector<double> mono_exp_intensities(peptide_size, 0);
410 std::vector<double> isotope_exp_intensities(peptide_size, 0);
411 for(const PeakIonIsotopeMatch &peak_ion_match : ion_isotope_list)
412 {
413 if(peak_ion_match.getPeptideIonType() == ion_type)
414 {
415 std::size_t vector_position =
416 peak_ion_match.getPeptideFragmentIonSp().get()->size() - 1;
417 PeptideNaturalIsotopeAverageSp iso_average_sp =
418 peak_ion_match.getPeptideNaturalIsotopeAverageSp();
419 if(iso_average_sp.get()->getIsotopeNumber() == 0)
420 {
421 mono_th_intensities[vector_position] =
422 iso_average_sp.get()->getIntensityRatio();
423 mono_exp_intensities[vector_position] =
424 peak_ion_match.getPeak().y;
425 }
426 else if(iso_average_sp.get()->getIsotopeNumber() == 1)
427 {
428 isotope_th_intensities[vector_position] =
429 iso_average_sp.get()->getIntensityRatio();
430 isotope_exp_intensities[vector_position] =
431 peak_ion_match.getPeak().y;
432 }
433 }
434 }
435
436 for(std::size_t i = 0; i < mono_th_intensities.size(); i++)
437 {
438 if((mono_th_intensities[i] != 0) && (isotope_th_intensities[i] != 0))
439 {
440 DataPoint xy(mono_th_intensities[i] / isotope_th_intensities[i],
441 mono_exp_intensities[i] /
442 isotope_exp_intensities[i]);
443 scaterplot.push_back(xy);
444 }
445 }
446 }
447
448 scaterplot.sortX();
449
450 LinearRegression linear_regression(scaterplot);
451
452 return linear_regression;
453}
A simple container of DataPoint instances.
Definition trace.h:148
void sortX(SortOrder sort_order=SortOrder::ascending)
Definition trace.cpp:1086
PeptideIon
PeptideIon enum defines all types of ions (Nter or Cter)
Definition types.h:427
@ xy
(x,y) format
std::shared_ptr< const PeptideNaturalIsotopeAverage > PeptideNaturalIsotopeAverageSp

References pappso::Trace::sortX(), and pappso::xy.

◆ getIonPairPrecursorMassDelta()

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

Definition at line 351 of file psmfeatures.cpp.

354{
355 qDebug() << m_precursorTheoreticalMz << " " << ion_pair.first.getPeak().x
356 << " " << ion_pair.second.getPeak().x << " "
357 << ion_pair.second.getCharge() << " " << ion_pair.first.getCharge()
358 << " " << m_parentCharge;
359 double diff =
360 (m_precursorTheoreticalMass + (MHPLUS * ion_pair.first.getCharge())) /
361 ion_pair.first.getCharge();
362
363
364 return (diff - (ion_pair.first.getPeak().x + ion_pair.second.getPeak().x -
365 ((MHPLUS * ion_pair.first.getCharge())) /
366 ion_pair.first.getCharge()));
367}
double m_precursorTheoreticalMz
unsigned int m_parentCharge
double m_precursorTheoreticalMass
const pappso_double MHPLUS(1.007276466879)

References pappso::MHPLUS().

◆ getMatchedMzDiffMean()

double pappso::PsmFeatures::getMatchedMzDiffMean ( ) const

get mean deviation of matched peak mass delta

Definition at line 199 of file psmfeatures.cpp.

200{
201 return m_matchedMzDiffMean;
202}

◆ getMatchedMzDiffSd()

double pappso::PsmFeatures::getMatchedMzDiffSd ( ) const

get standard deviation of matched peak mass delta

Definition at line 193 of file psmfeatures.cpp.

194{
195 return m_matchedMzDiffSd;
196}

◆ getMaxConsecutiveIon()

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

get the maximum consecutive fragments of one ion type

Parameters
ion_typeion species (y, b, ...)

Definition at line 212 of file psmfeatures.cpp.

213{
214 std::size_t max = 0;
215 auto peak_ion_match_list =
216 msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList();
217
218 peak_ion_match_list.erase(
219 std::remove_if(
220 peak_ion_match_list.begin(),
221 peak_ion_match_list.end(),
222 [ion_type](const PeakIonIsotopeMatch &a) {
223 if(a.getPeptideIonType() != ion_type)
224 return true;
225 if(a.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber() > 0)
226 return true;
227 return false;
228 }),
229 peak_ion_match_list.end());
230
231 peak_ion_match_list.sort(
232 [](const PeakIonIsotopeMatch &a, const PeakIonIsotopeMatch &b) {
233 if(a.getCharge() < b.getCharge())
234 return true;
235 if(a.getPeptideIonType() < b.getPeptideIonType())
236 return true;
237 if(a.getPeptideFragmentIonSp().get()->size() <
238 b.getPeptideFragmentIonSp().get()->size())
239 return true;
240 return false;
241 });
242
243 unsigned int charge = 0;
244 std::size_t size = 0;
245 std::size_t count = 0;
246 for(std::list<PeakIonIsotopeMatch>::iterator it = peak_ion_match_list.begin();
247 it != peak_ion_match_list.end();
248 it++)
249 {
250 qDebug()
251 << it->toString() << max << " " << it->getPeak().x << " "
252 << it->getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber();
253 count++;
254 if((charge != it->getCharge()) ||
255 (size != (it->getPeptideFragmentIonSp().get()->size() - 1)))
256 {
257 count = 1;
258 charge = it->getCharge();
259 }
260 if(max < count)
261 max = count;
262
263 size = it->getPeptideFragmentIonSp().get()->size();
264 }
265
266 return max;
267}
@ max
maximum of intensities

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 330 of file psmfeatures.cpp.

332{
333 auto peak_it = std::max_element(
334 m_peakIonPairs.begin(),
335 m_peakIonPairs.end(),
336 [](const std::pair<pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch>
337 &a,
338 const std::pair<pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch>
339 &b) {
340 return ((a.first.getPeak().y + a.second.getPeak().y) <
341 (b.first.getPeak().y + b.second.getPeak().y));
342 });
343
344 if(peak_it == m_peakIonPairs.end())
345 return 0;
346
347 return getIonPairPrecursorMassDelta(*peak_it);
348}
double getIonPairPrecursorMassDelta(const std::pair< pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch > &ion_pair) const

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

◆ getMaxIntensityPeakIonMatch()

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

Definition at line 308 of file psmfeatures.cpp.

310{
311 std::list<pappso::PeakIonIsotopeMatch> peak_ion_type =
312 msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList();
313
314 peak_ion_type.remove_if([ion_type](const PeakIonIsotopeMatch &a) {
315 return (a.getPeptideIonType() != ion_type);
316 });
317 auto peak_it = std::max_element(
318 peak_ion_type.begin(),
319 peak_ion_type.end(),
320 [](const PeakIonIsotopeMatch &a, const PeakIonIsotopeMatch &b) {
321 return (a.getPeak().y < b.getPeak().y);
322 });
323
324 if(peak_it == peak_ion_type.end())
325 return 0;
326 return peak_it->getPeak().y;
327}

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

◆ getNumberOfMatchedIons()

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

number of matched ions (peaks)

Definition at line 206 of file psmfeatures.cpp.

207{
208 return msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList().size();
209}

◆ getPeakIonPairs()

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

Definition at line 174 of file psmfeatures.cpp.

175{
176 return m_peakIonPairs;
177}

◆ getTotalIntensity()

double PsmFeatures::getTotalIntensity ( ) const

sum of all peak intensities (matched or not)

Definition at line 161 of file psmfeatures.cpp.

162{
164}
double m_spectrumSumIntensity

References m_spectrumSumIntensity.

◆ getTotalIntensityOfMatchedIonComplementPairs()

double pappso::PsmFeatures::getTotalIntensityOfMatchedIonComplementPairs ( ) const

intensity of matched ion complement

Definition at line 180 of file psmfeatures.cpp.

181{
182
183 double sum = 0;
184 for(auto &peak_pairs : m_peakIonPairs)
185 {
186 sum += peak_pairs.first.getPeak().y;
187 sum += peak_pairs.second.getPeak().y;
188 }
189 return sum;
190}

References pappso::sum.

◆ getTotalIntensityOfMatchedIons()

double PsmFeatures::getTotalIntensityOfMatchedIons ( ) const

sum of matched peak intensities

Definition at line 150 of file psmfeatures.cpp.

151{
152 double sum = 0;
153 for(const PeakIonMatch &peak_ion_match : *msp_peptideSpectrumMatch.get())
154 {
155 sum += peak_ion_match.getPeak().y;
156 }
157 return sum;
158}

References msp_peptideSpectrumMatch, and pappso::sum.

◆ setPeptideSpectrumCharge()

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

Definition at line 58 of file psmfeatures.cpp.

62{
63 m_peakIonPairs.clear();
64 msp_peptide = peptideSp;
65 MassSpectrum spectrum(*p_spectrum);
66 msp_filterKeepGreater.get()->filter(spectrum);
67 // msp_filterChargeDeconvolution.get()->filter(spectrum);
68 // msp_filterMzExclusion.get()->filter(spectrum);
69
71 std::make_shared<PeptideIsotopeSpectrumMatch>(spectrum,
72 peptideSp,
73 parent_charge,
76 max_isotope_number,
77 1);
78
79 msp_peptideSpectrumMatch.get()->dropPeaksLackingMonoisotope();
80 m_spectrumSumIntensity = spectrum.sumY();
81
82
83 qDebug() << " accumulate";
84 std::vector<double> delta_list;
85
86
87 // TODO compute number of matched complementary peaks having m/z compatible
88 // with the precursor
89
90 m_precursorTheoreticalMz = peptideSp.get()->getMz(parent_charge);
91 m_precursorTheoreticalMass = peptideSp.get()->getMass();
92 m_parentCharge = parent_charge;
93
94
95 findComplementIonPairs(peptideSp);
96
97
98 for(const pappso::PeakIonIsotopeMatch &peak_ion :
99 msp_peptideSpectrumMatch.get()->getPeakIonIsotopeMatchList())
100 {
101 delta_list.push_back(
102 peak_ion.getPeptideFragmentIonSp().get()->getMz(peak_ion.getCharge()) -
103 peak_ion.getPeak().x);
104 }
106 std::accumulate(delta_list.begin(), delta_list.end(), 0);
107
108 qDebug() << " delta_list.size()=" << delta_list.size();
112 if(delta_list.size() > 0)
113 {
114 m_matchedMzDiffMean = sum / ((pappso::pappso_double)delta_list.size());
115
116 std::sort(delta_list.begin(), delta_list.end());
117 m_matchedMzDiffMedian = delta_list[(delta_list.size() / 2)];
118
119
120 qDebug() << " sd";
122 for(pappso::pappso_double val : delta_list)
123 {
124 // sd = sd + ((val - mean) * (val - mean));
125 m_matchedMzDiffSd += std::pow((val - m_matchedMzDiffMean), 2);
126 }
127 m_matchedMzDiffSd = m_matchedMzDiffSd / delta_list.size();
129 }
130 else
131 {
132 }
133}
Class to represent a mass spectrum.
void findComplementIonPairs(const pappso::PeptideSp &peptideSp)
double pappso_double
A type definition for doubles.
Definition types.h:50

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 151 of file psmfeatures.h.

Referenced by PsmFeatures(), and setPeptideSpectrumCharge().

◆ m_matchedMzDiffMean

double pappso::PsmFeatures::m_matchedMzDiffMean = 0
private

Definition at line 163 of file psmfeatures.h.

Referenced by setPeptideSpectrumCharge().

◆ m_matchedMzDiffMedian

double pappso::PsmFeatures::m_matchedMzDiffMedian = 0
private

Definition at line 164 of file psmfeatures.h.

Referenced by setPeptideSpectrumCharge().

◆ m_matchedMzDiffSd

double pappso::PsmFeatures::m_matchedMzDiffSd = 0
private

Definition at line 165 of file psmfeatures.h.

Referenced by setPeptideSpectrumCharge().

◆ m_ms2precision

PrecisionPtr pappso::PsmFeatures::m_ms2precision
private

Definition at line 150 of file psmfeatures.h.

Referenced by PsmFeatures(), and setPeptideSpectrumCharge().

◆ m_parentCharge

unsigned int pappso::PsmFeatures::m_parentCharge = 1
private

Definition at line 157 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 161 of file psmfeatures.h.

Referenced by setPeptideSpectrumCharge().

◆ m_precursorTheoreticalMass

double pappso::PsmFeatures::m_precursorTheoreticalMass
private

Definition at line 156 of file psmfeatures.h.

Referenced by setPeptideSpectrumCharge().

◆ m_precursorTheoreticalMz

double pappso::PsmFeatures::m_precursorTheoreticalMz
private

Definition at line 155 of file psmfeatures.h.

Referenced by setPeptideSpectrumCharge().

◆ m_spectrumSumIntensity

double pappso::PsmFeatures::m_spectrumSumIntensity
private

Definition at line 153 of file psmfeatures.h.

Referenced by getTotalIntensity(), and setPeptideSpectrumCharge().

◆ msp_filterChargeDeconvolution

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

Definition at line 143 of file psmfeatures.h.

Referenced by PsmFeatures().

◆ msp_filterKeepGreater

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

Definition at line 145 of file psmfeatures.h.

Referenced by PsmFeatures(), and setPeptideSpectrumCharge().

◆ msp_filterMzExclusion

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

Definition at line 144 of file psmfeatures.h.

Referenced by PsmFeatures().

◆ msp_peptide

pappso::PeptideSp pappso::PsmFeatures::msp_peptide
private

Definition at line 148 of file psmfeatures.h.

Referenced by setPeptideSpectrumCharge().

◆ msp_peptideSpectrumMatch

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

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