libpappsomspp
Library for mass spectrometry
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peptidespectrum.cpp
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1/**
2 * \file pappsomspp/processing/specglob/peptidespectrum.cpp
3 * \date 06/11/2023
4 * \author Olivier Langella
5 * \brief transform a peptide to SpecGlob spectrum
6 *
7 * C++ implementation of the SpecGlob algorithm described in :
8 * 1. Prunier, G. et al. Fast alignment of mass spectra in large proteomics
9 * datasets, capturing dissimilarities arising from multiple complex
10 * modifications of peptides. BMC Bioinformatics 24, 421 (2023).
11 *
12 * HAL Id : hal-04296170 , version 1
13 * Mot de passe : hxo20cl
14 * DOI : 10.1186/s12859-023-05555-y
15 */
16
17
18/*
19 * SpecGlobTool, Spectra to peptide alignment tool
20 * Copyright (C) 2023 Olivier Langella
21 * <olivier.langella@universite-paris-saclay.fr>
22 *
23 * This program is free software: you can redistribute it and/or modify
24 * it under the terms of the GNU General Public License as published by
25 * the Free Software Foundation, either version 3 of the License, or
26 * (at your option) any later version.
27 *
28 * This program is distributed in the hope that it will be useful,
29 * but WITHOUT ANY WARRANTY; without even the implied warranty of
30 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
31 * GNU General Public License for more details.
32 *
33 * You should have received a copy of the GNU General Public License
34 * along with this program. If not, see <http://www.gnu.org/licenses/>.
35 *
36 */
37
38#include "peptidespectrum.h"
39#include "../../peptide/peptidefragmentionlistbase.h"
40#include "../../peptide/peptiderawfragmentmasses.h"
41
42namespace pappso
43{
44namespace specglob
45{
47 : std::vector<PeptideSpectrumDataPoint>()
48{
50 msp_peptide = peptide_sp;
51 std::list<pappso::PeptideIon> ion_list;
52 ion_list.push_back(ion_type);
53
54
55 pappso::PeptideFragmentIonListBase fragmented_ion_list(msp_peptide, ion_list);
56
57 std::list<pappso::PeptideFragmentIonSp> peptide_ion_list =
59
60 push_back({pappso::MHPLUS, 0});
61 // qDebug() << pappso::PeptideRawFragmentMasses::getDeltaMass(ion_type);
62 for(auto &peptide_ion : peptide_ion_list)
63 {
64 push_back({peptide_ion.get()->getMz(1), 0});
65 }
66 push_back({(msp_peptide.get()->getMz(1) - pappso::MASSH2O +
68 0});
69 for(std::size_t i = 1; i < size(); i++)
70 {
71 at(i).diff_mz = (at(i).mz - at(i - 1).mz);
72 }
73}
74
76 : std::vector<PeptideSpectrumDataPoint>(other)
77{
79}
80
84
85std::vector<double>
87{
88 std::vector<double> mass_list;
89 for(const PeptideSpectrumDataPoint &n : *this)
90 {
91 mass_list.push_back(n.mz);
92 };
93
94 return mass_list;
95}
96
99{
100 return msp_peptide;
101}
102} // namespace specglob
103} // namespace pappso
const std::list< PeptideFragmentIonSp > getPeptideFragmentIonSp(PeptideIon ion_type) const
static pappso_double getDeltaMass(PeptideIon ion_type)
pappso::PeptideSp getPeptideSp() const
std::vector< double > getMassList() const
PeptideSpectrum(const pappso::PeptideSp peptide_sp)
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:425
@ b
Nter acylium ions.
std::shared_ptr< const Peptide > PeptideSp
const pappso_double MHPLUS(1.007276466879)
const pappso_double MASSH2O((MPROTIUM *2)+MASSOXYGEN)
transform a peptide to SpecGlob spectrum