libpappsomspp
Library for mass spectrometry
peptiderawfragmentmasses.cpp
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1 /**
2  * \file pappsomspp/peptide/peptiderawfragmentmasses.cpp
3  * \date 16/7/2016
4  * \author Olivier Langella
5  * \brief class dedicated to raw mass computations of peptide products
6  * (fragments)
7  */
8 
9 /*******************************************************************************
10  * Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
11  *
12  * This file is part of the PAPPSOms++ library.
13  *
14  * PAPPSOms++ is free software: you can redistribute it and/or modify
15  * it under the terms of the GNU General Public License as published by
16  * the Free Software Foundation, either version 3 of the License, or
17  * (at your option) any later version.
18  *
19  * PAPPSOms++ is distributed in the hope that it will be useful,
20  * but WITHOUT ANY WARRANTY; without even the implied warranty of
21  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
22  * GNU General Public License for more details.
23  *
24  * You should have received a copy of the GNU General Public License
25  * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
26  *
27  * Contributors:
28  * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
29  *implementation
30  ******************************************************************************/
31 
33 namespace pappso
34 {
35 
36 
39  [(std::int8_t)PeptideIon::b] = 0,
40  [(std::int8_t)PeptideIon::bstar] = -MASSNH3,
41  [(std::int8_t)PeptideIon::bo] = -MASSH2O,
42  [(std::int8_t)PeptideIon::a] = -MASSCO,
43  [(std::int8_t)PeptideIon::astar] = -MASSCO - MASSNH3,
44  [(std::int8_t)PeptideIon::ao] = -MASSCO - MASSH2O,
45  [(std::int8_t)PeptideIon::bp] = -1,
46  [(std::int8_t)PeptideIon::c] = MASSNH3,
47  [(std::int8_t)PeptideIon::y] = MASSH2O,
48  [(std::int8_t)PeptideIon::ystar] = MASSH2O - MASSNH3,
49  [(std::int8_t)PeptideIon::yo] = 0,
50  [(std::int8_t)PeptideIon::z] = MASSOXYGEN - MASSNITROGEN - MPROTIUM,
51  [(std::int8_t)PeptideIon::yp] = -1,
52  [(std::int8_t)PeptideIon::x] = MASSCO + MASSOXYGEN};
53 
54 
57 {
58  return m_ionDeltaMz[(std::int8_t)ion_type];
59 }
60 
61 
64 {
65 
66  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
67  std::vector<Aa>::const_iterator it(peptide.begin());
68  std::vector<Aa>::const_iterator end(peptide.end());
69  if(it == end)
70  return;
71 
72  pappso_double nter_internal =
74  pappso_double cter_internal =
76  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
77  pappso_double cumulative_mass = it->getMass() - nter_internal;
78  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
79  m_cumulativeNterMasses.push_back(cumulative_mass);
80  it++;
81 
82  if(it != end)
83  {
84  end--;
85  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
86  while(it != end)
87  {
88 
89  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
90  << " cumulative_mass=" << cumulative_mass;
91  cumulative_mass += it->getMass();
93  (it->getLetter() == 'P'))
94  {
95  }
96  else
97  {
98  m_cumulativeNterMasses.push_back(cumulative_mass);
99  }
100  it++;
101  }
102  }
103 
104  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
105  std::vector<Aa>::const_reverse_iterator rit(peptide.rbegin());
106  std::vector<Aa>::const_reverse_iterator ritf(peptide.rbegin());
107  std::vector<Aa>::const_reverse_iterator rend(peptide.rend());
108  ritf++;
109  cumulative_mass = rit->getMass() - cter_internal;
110  if((mode == RawFragmentationMode::proline_effect) && (ritf != rend) &&
111  (ritf->getLetter() == 'P'))
112  {
113  }
114  else
115  {
116  m_cumulativeCterMasses.push_back(cumulative_mass);
117  }
118  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
119 
120  rit++;
121  ritf++;
122  if(rit != rend)
123  {
124  rend--;
125  while(rit != rend)
126  {
127  cumulative_mass += rit->getMass();
129  (ritf != peptide.rend()) && (ritf->getLetter() == 'P'))
130  {
131  }
132  else
133  {
134  m_cumulativeCterMasses.push_back(cumulative_mass);
135  }
136  rit++;
137  ritf++;
138  }
139  }
140 
141  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
142 }
143 
144 void
146  std::vector<pappso_double> &mass_list, PeptideIon ion_type) const
147 {
148  const std::vector<pappso_double> *p_mass_list = &m_cumulativeCterMasses;
149 
150  if(peptideIonIsNter(ion_type))
151  {
152  // nter
153  p_mass_list = &m_cumulativeNterMasses;
154  }
155 
156  for(pappso_double mass : *p_mass_list)
157  {
158  mass_list.push_back(mass + m_ionDeltaMz[(std::int8_t)ion_type]);
159  }
160 }
161 
162 void
163 PeptideRawFragmentMasses::pushBackIonMz(std::vector<pappso_double> &mass_list,
164  PeptideIon ion_type,
165  unsigned int charge) const
166 {
167  const std::vector<pappso_double> *p_mass_list = &m_cumulativeCterMasses;
168 
169  if(peptideIonIsNter(ion_type))
170  {
171  // nter
172  p_mass_list = &m_cumulativeNterMasses;
173  }
174 
175  for(pappso_double mass : *p_mass_list)
176  {
177  mass_list.push_back(
178  (mass + m_ionDeltaMz[(std::int8_t)ion_type] + (MHPLUS * charge)) /
179  charge);
180  }
181 }
182 
183 void
185  std::vector<SimplePeakIonMatch> &peak_match_list,
186  const MassSpectrum &spectrum,
187  PrecisionPtr precision,
188  PeptideIon ion_type,
189  unsigned int charge) const
190 {
191  std::vector<pappso_double> mass_list;
192  pushBackIonMz(mass_list, ion_type, charge);
193 
194  // no need to sort
195  // std::sort(mass_list.begin(), mass_list.end());
196 
197  std::vector<pappso_double>::iterator it_mz = mass_list.begin();
198  std::vector<pappso_double>::iterator it_mz_end = mass_list.end();
199 
200  // scan products over each peak in spectrum :
201  std::vector<DataPoint>::const_iterator it_peak = spectrum.begin();
202  std::vector<DataPoint>::const_iterator it_peak_end = spectrum.end();
203  unsigned int ion_size = 1;
204  while((it_peak != it_peak_end) && (it_mz != it_mz_end))
205  {
206  MzRange massrange(it_peak->x, precision);
207  if((*it_mz) > massrange.upper())
208  {
209  it_peak++;
210  continue;
211  }
212  if((*it_mz) < massrange.lower())
213  {
214  it_mz++;
215  ion_size++;
216  continue;
217  }
218  peak_match_list.push_back(
219  {(*it_peak), ion_type, ion_size, charge, (*it_mz)});
220  it_mz++;
221  ion_size++;
222  }
223 }
224 
226 {
227 }
228 } // namespace pappso
pappso_double getMass() const
Class to represent a mass spectrum.
Definition: massspectrum.h:71
pappso_double lower() const
Definition: mzrange.h:71
pappso_double upper() const
Definition: mzrange.h:77
static pappso_double getDeltaMass(PeptideIon ion_type)
void pushBackMatchSpectrum(std::vector< SimplePeakIonMatch > &peak_match_list, const MassSpectrum &spectrum, PrecisionPtr precision, PeptideIon ion_type, unsigned int charge) const
PeptideRawFragmentMasses(const Peptide &peptide, RawFragmentationMode mode)
std::vector< pappso_double > m_cumulativeCterMasses
cumulative Cter masses (without internal Cter modification)
std::vector< pappso_double > m_cumulativeNterMasses
cumulative Nter masses (without internal Nter modification)
void pushBackIonMz(std::vector< pappso_double > &mass_list, PeptideIon ion_type, unsigned int charge) const
void pushBackIonMasses(std::vector< pappso_double > &mass_list, PeptideIon ion_type) const
static ionDeltatMzMassMap m_ionDeltaMz
std::vector< Aa >::iterator end()
Definition: peptide.h:139
AaModificationP getInternalNterModification() const
Definition: peptide.cpp:400
std::vector< Aa >::const_reverse_iterator rend() const
Definition: peptide.h:163
std::vector< Aa >::const_reverse_iterator rbegin() const
Definition: peptide.h:157
AaModificationP getInternalCterModification() const
Definition: peptide.cpp:411
std::vector< Aa >::iterator begin()
Definition: peptide.h:133
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
PeptideIon
PeptideIon enum defines all types of ions (Nter or Cter)
Definition: types.h:386
@ a
Nter aldimine ions.
@ y
Cter amino ions.
@ c
Nter amino ions.
@ astar
Nter aldimine ions + NH3 loss.
@ ystar
Cter amino ions + NH3 loss.
@ yo
Cter amino ions + H2O loss.
@ bstar
Nter acylium ions + NH3 loss.
@ b
Nter acylium ions.
@ x
Cter acylium ions.
@ bo
Nter acylium ions + H2O loss.
@ ao
Nter aldimine ions + H2O loss.
@ z
Cter carbocations.
const pappso_double MASSCO(MASSCARBON+MASSOXYGEN)
const pappso_double MHPLUS(1.007276466879)
double pappso_double
A type definition for doubles.
Definition: types.h:49
const pappso_double MPROTIUM(1.007825032241)
const pappso_double MASSH2O((MPROTIUM *2)+MASSOXYGEN)
const pappso_double MASSNH3((MPROTIUM *3)+MASSNITROGEN)
const pappso_double MASSNITROGEN(14.0030740048)
const pappso_double MASSOXYGEN(15.99491461956)
bool peptideIonIsNter(PeptideIon ion_type)
tells if an ion is Nter
Definition: peptide.cpp:60
class dedicated to raw mass computations of peptide products (fragments)