libpappsomspp
Library for mass spectrometry
pappso::PsmFeatures Class Reference

#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, unsigned int max_isotope_number)
 
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
 
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
Definition: precision.cpp:205
std::shared_ptr< FilterChargeDeconvolution > msp_filterChargeDeconvolution
Definition: psmfeatures.h:143
std::shared_ptr< FilterResampleKeepGreater > msp_filterKeepGreater
Definition: psmfeatures.h:145
std::shared_ptr< FilterMzExclusion > msp_filterMzExclusion
Definition: psmfeatures.h:144
std::list< PeptideIon > m_ionList
Definition: psmfeatures.h:151
PrecisionPtr m_ms2precision
Definition: psmfeatures.h:150
@ 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
Definition: psmfeatures.h:161

◆ 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
Definition: psmfeatures.h:147
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
Definition: psmfeatures.h:148

◆ 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:425
@ 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
Definition: psmfeatures.h:155
unsigned int m_parentCharge
Definition: psmfeatures.h:157
double m_precursorTheoreticalMass
Definition: psmfeatures.h:156
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}
double m_matchedMzDiffMean
Definition: psmfeatures.h:163

◆ 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
Definition: psmfeatures.h:153

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.
Definition: massspectrum.h:71
void findComplementIonPairs(const pappso::PeptideSp &peptideSp)
double m_matchedMzDiffMedian
Definition: psmfeatures.h:164
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: