libpappsomspp
Library for mass spectrometry
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pappso::specglob::PostTreatment Class Reference

#include <posttreatment.h>

Public Member Functions

 PostTreatment (pappso::PrecisionPtr precision, const PeptideModel &peptide_model)
virtual ~PostTreatment ()
const PeptideModel & getBetterPeptideModel () const
const PeptideModel & getOriginalPeptideModel () const
bool findReplaceMutations ()

Private Member Functions

void findBetterPeptideModel ()
 whole processus to find a better peptide model
void tryBetterPositionOffsets ()
 try to move offset (mass difference)
void tryToRemoveOffsets ()
 try to remove offset (mass difference)
void tryToCumulateOffSets ()
 try to assign residual mass delta to non aligned elements

Private Attributes

PeptideModel m_originalPeptideModel
PeptideModel m_betterPeptideModel
pappso::PrecisionPtr m_precision

Detailed Description

Todo
write docs

Definition at line 52 of file posttreatment.h.

Constructor & Destructor Documentation

◆ PostTreatment()

pappso::specglob::PostTreatment::PostTreatment ( pappso::PrecisionPtr precision,
const PeptideModel & peptide_model )

Default constructor

Definition at line 45 of file posttreatment.cpp.

46 : m_originalPeptideModel(peptide_model), m_betterPeptideModel(peptide_model)
47{
48 m_precision = precision;
49 m_originalPeptideModel.matchExperimentalPeaks(m_precision);
50
51 findBetterPeptideModel();
52}
pappso::specglob::PostTreatment::m_precision
pappso::PrecisionPtr m_precision
Definition posttreatment.h:114
pappso::specglob::PostTreatment::findBetterPeptideModel
void findBetterPeptideModel()
whole processus to find a better peptide model
Definition posttreatment.cpp:65

References findBetterPeptideModel(), m_betterPeptideModel, m_originalPeptideModel, and m_precision.

◆ ~PostTreatment()

pappso::specglob::PostTreatment::~PostTreatment ( )
virtual

Destructor

Definition at line 54 of file posttreatment.cpp.

55{
56}

Member Function Documentation

◆ findBetterPeptideModel()

void pappso::specglob::PostTreatment::findBetterPeptideModel ( )
private

whole processus to find a better peptide model

assign residual mass to Cter remove complementary mass delta eliminate negative offsets (perhaps neutral loss) check negative offsets for amino acid mass sums to remove try better positions for mass delta

Definition at line 65 of file posttreatment.cpp.

66{
67 if(std::abs(m_originalPeptideModel.getMassDelta()) > m_precision->getNominal())
68 {
69 // calculate the number of shared peaks with the deltaM on the last aa
70 m_betterPeptideModel.assignResidualMass2Cter();
71 m_betterPeptideModel.matchExperimentalPeaks(m_precision);
72 if(m_betterPeptideModel.getCountSharedPeaks() > m_originalPeptideModel.getCountSharedPeaks())
73 {
74 }
75 else
76 {
77 // not better, get back to original peptide
78 m_betterPeptideModel.copyDeep(m_originalPeptideModel);
79 }
80 }
81 else
82 {
83 m_betterPeptideModel.matchExperimentalPeaks(m_precision);
84 }
85
86
87 // Try to remove complementary mass offset
88 // Not done if the number of peaks is increased by more than two peaks
89 // If the number of peaks > +2, it is considered as an information that must
90 // be kept in the alignment Could be modified...the information is in the
91 // preAligned column
92 PeptideModel test_peptide_model_remove_complementary(m_betterPeptideModel);
93 if(test_peptide_model_remove_complementary.eliminateComplementaryDelta(m_precision))
94 {
95
96 test_peptide_model_remove_complementary.matchExperimentalPeaks(m_precision);
97
98 qDebug() << "test_peptide_model_remove_complementary.getCountSharedPeaks()="
99 << test_peptide_model_remove_complementary.getCountSharedPeaks()
100 << " m_betterPeptideModel.getCountSharedPeaks()="
101 << m_betterPeptideModel.getCountSharedPeaks();
102 if(test_peptide_model_remove_complementary.getCountSharedPeaks() <
103 m_betterPeptideModel.getCountSharedPeaks() + 2)
104 {
105 qDebug() << "replace with " << test_peptide_model_remove_complementary.toString();
106 m_betterPeptideModel.copyDeep(test_peptide_model_remove_complementary);
107 }
108 }
109
110 // if bestModified contains negative offSet, try to remove amino acids to
111 // explain it
112 PeptideModel test_peptide_model_remove_negative = m_betterPeptideModel;
113 if(test_peptide_model_remove_negative.eliminateNegativeOffset(m_precision))
114 {
115 test_peptide_model_remove_negative.matchExperimentalPeaks(m_precision);
116 if(test_peptide_model_remove_negative.getCountSharedPeaks() >=
117 m_betterPeptideModel.getCountSharedPeaks())
118 {
119 qDebug() << "replace with " << test_peptide_model_remove_negative.toString();
120 m_betterPeptideModel.copyDeep(test_peptide_model_remove_negative);
121 }
122 }
123
124 // findBetterMassDifferencePosition
125 tryToRemoveOffsets();
126 tryBetterPositionOffsets();
127
128
129 if(m_betterPeptideModel.getMassDelta() < -m_precision->getNominal())
130 {
131 tryToCumulateOffSets();
132 }
133
134 m_betterPeptideModel.removeBracketsForAlignedAA();
135}
pappso::specglob::PostTreatment::tryToCumulateOffSets
void tryToCumulateOffSets()
try to assign residual mass delta to non aligned elements
Definition posttreatment.cpp:240
pappso::specglob::PostTreatment::tryToRemoveOffsets
void tryToRemoveOffsets()
try to remove offset (mass difference)
Definition posttreatment.cpp:201
pappso::specglob::PostTreatment::tryBetterPositionOffsets
void tryBetterPositionOffsets()
try to move offset (mass difference)
Definition posttreatment.cpp:138

References pappso::specglob::PeptideModel::eliminateComplementaryDelta(), pappso::specglob::PeptideModel::eliminateNegativeOffset(), pappso::specglob::PeptideModel::getCountSharedPeaks(), m_betterPeptideModel, m_originalPeptideModel, m_precision, pappso::specglob::PeptideModel::matchExperimentalPeaks(), pappso::specglob::PeptideModel::toString(), tryBetterPositionOffsets(), tryToCumulateOffSets(), and tryToRemoveOffsets().

Referenced by PostTreatment().

◆ findReplaceMutations()

bool pappso::specglob::PostTreatment::findReplaceMutations ( )

Definition at line 281 of file posttreatment.cpp.

282{
283 auto peptide_model = m_betterPeptideModel;
284
285 bool modif = false;
286 std::vector<Enums::AminoAcidChar> aa_list = {Enums::AminoAcidChar::alanine,
287 Enums::AminoAcidChar::aspartic_acid,
288 Enums::AminoAcidChar::glutamic_acid,
289 Enums::AminoAcidChar::phenylalanine,
290 Enums::AminoAcidChar::glycine,
291 Enums::AminoAcidChar::histidine,
292 Enums::AminoAcidChar::isoleucine,
293 Enums::AminoAcidChar::lysine,
294 Enums::AminoAcidChar::leucine,
295 Enums::AminoAcidChar::methionine,
296 Enums::AminoAcidChar::asparagine,
297 Enums::AminoAcidChar::proline,
298 Enums::AminoAcidChar::glutamine,
299 Enums::AminoAcidChar::arginine,
300 Enums::AminoAcidChar::serine,
301 Enums::AminoAcidChar::threonine,
302 Enums::AminoAcidChar::valine,
303 Enums::AminoAcidChar::tryptophan,
304 Enums::AminoAcidChar::tyrosine};
305 if(peptide_model.checkForMutations(aa_list, m_precision))
306 {
307 modif = true;
308 }
309 pappso::Aa cysteine('C');
310 cysteine.addAaModification(pappso::AaModification::getInstance("MOD:00397")); // carbamido
311 if(peptide_model.checkForMutation(cysteine, m_precision))
312 {
313 modif = true;
314 }
315 pappso::Aa methionine('M');
316 methionine.addAaModification(pappso::AaModification::getInstance("MOD:00719")); // oxydation
317 if(peptide_model.checkForMutation(methionine, m_precision))
318 {
319 modif = true;
320 }
321 if(modif)
322 {
323 m_betterPeptideModel = peptide_model;
324 }
325 return modif;
326}
pappso::AaModification::getInstance
static AaModificationP getInstance(const QString &accession)
Definition aamodification.cpp:368

References pappso::Enums::alanine, pappso::Enums::arginine, pappso::Enums::asparagine, pappso::Enums::aspartic_acid, pappso::AaModification::getInstance(), pappso::Enums::glutamic_acid, pappso::Enums::glutamine, pappso::Enums::glycine, pappso::Enums::histidine, pappso::Enums::isoleucine, pappso::Enums::leucine, pappso::Enums::lysine, m_betterPeptideModel, m_precision, pappso::Enums::methionine, pappso::Enums::phenylalanine, pappso::Enums::proline, pappso::Enums::serine, pappso::Enums::threonine, pappso::Enums::tryptophan, pappso::Enums::tyrosine, and pappso::Enums::valine.

Referenced by pappso::cbor::psm::PsmSpecGlobScan::process().

◆ getBetterPeptideModel()

const PeptideModel & pappso::specglob::PostTreatment::getBetterPeptideModel ( ) const

Definition at line 59 of file posttreatment.cpp.

60{
61 return m_betterPeptideModel;
62}

References m_betterPeptideModel.

Referenced by pappso::cbor::psm::PsmSpecGlobScan::process().

◆ getOriginalPeptideModel()

const PeptideModel & pappso::specglob::PostTreatment::getOriginalPeptideModel ( ) const

Definition at line 275 of file posttreatment.cpp.

276{
277 return m_originalPeptideModel;
278}

References m_originalPeptideModel.

◆ tryBetterPositionOffsets()

void pappso::specglob::PostTreatment::tryBetterPositionOffsets ( )
private

try to move offset (mass difference)

for each mass difference position, try to move to other position if the amino acid is not aligned, count matched peaks and compare to the previous solution. Keep only the better position

Definition at line 138 of file posttreatment.cpp.

139{
140
141 PeptideModel better_peptide_model_move_offset = m_betterPeptideModel;
142 std::size_t best_count_shared_peaks = m_betterPeptideModel.getCountSharedPeaks();
143 qDebug() << best_count_shared_peaks;
144
145 qDebug() << m_betterPeptideModel.toString();
146 bool move = false;
147 for(std::size_t i = 0; i < m_betterPeptideModel.size(); i++)
148 {
149
150 qDebug() << "i =" << i;
151 if(m_betterPeptideModel.at(i).remove == true)
152 continue;
153 if(m_betterPeptideModel.at(i).mass_difference == 0.0)
154 continue;
155 if(m_betterPeptideModel.at(i).bracket == true)
156 {
157 // try to move if
158 double mass_diff = m_betterPeptideModel.at(i).mass_difference;
159 PeptideModel test_peptide_model_move_offset = better_peptide_model_move_offset;
160 test_peptide_model_move_offset.at(i).mass_difference = 0;
161 qDebug() << test_peptide_model_move_offset.toString();
162
163 std::size_t j = i;
164 while(j > 0)
165 {
166 j -= 1;
167 if(test_peptide_model_move_offset.at(j).bracket == false)
168 break;
169 if(test_peptide_model_move_offset.at(j).mass_difference != 0.0)
170 break;
171
172 test_peptide_model_move_offset.at(j).mass_difference = mass_diff;
173 test_peptide_model_move_offset.matchExperimentalPeaks(m_precision);
174
175 qDebug() << test_peptide_model_move_offset.toString() << " "
176 << test_peptide_model_move_offset.getCountSharedPeaks() << " "
177 << best_count_shared_peaks;
178 if(test_peptide_model_move_offset.getCountSharedPeaks() > best_count_shared_peaks)
179 {
180 best_count_shared_peaks = test_peptide_model_move_offset.getCountSharedPeaks();
181 better_peptide_model_move_offset.copyDeep(test_peptide_model_move_offset);
182 move = true;
183 }
184 else
185 {
186 test_peptide_model_move_offset = better_peptide_model_move_offset;
187 }
188 }
189 }
190 }
191
192 if(move)
193 {
194 m_betterPeptideModel.copyDeep(better_peptide_model_move_offset);
195 }
196 qDebug() << m_betterPeptideModel.toString();
197}

References pappso::specglob::PeptideModel::copyDeep(), pappso::specglob::PeptideModel::getCountSharedPeaks(), m_betterPeptideModel, m_precision, pappso::specglob::PeptideModel::matchExperimentalPeaks(), and pappso::specglob::PeptideModel::toString().

Referenced by findBetterPeptideModel().

◆ tryToCumulateOffSets()

void pappso::specglob::PostTreatment::tryToCumulateOffSets ( )
private

try to assign residual mass delta to non aligned elements

This method is run only if there is not-aligned offSets. It may be explained by an inadequate alignment at the start because we give some advance to non-tryptic peptides. But, at the end of the alignment, we can consider it was not the best choice Trying to improve this alignment by adding not-aligned offSet with another one

Definition at line 240 of file posttreatment.cpp.

241{
242 double mass_delta = m_betterPeptideModel.getMassDelta();
243 std::size_t best_count_shared_peaks = m_betterPeptideModel.getCountSharedPeaks();
244 PeptideModel better_peptide_model_cumulating_residual_mass_delta;
245 for(std::size_t i = 0; i < m_betterPeptideModel.size(); i++)
246 {
247 if(m_betterPeptideModel.at(i).remove == true)
248 continue;
249 if(m_betterPeptideModel.at(i).mass_difference == 0.0)
250 continue;
251
252 PeptideModel test_peptide_model_cumulating_residual_mass_delta = m_betterPeptideModel;
253 // try to cumulate the current mass difference with unexplained mass delta
254 // :
255 test_peptide_model_cumulating_residual_mass_delta.at(i).mass_difference += mass_delta;
256 test_peptide_model_cumulating_residual_mass_delta.matchExperimentalPeaks(m_precision);
257 if(test_peptide_model_cumulating_residual_mass_delta.getCountSharedPeaks() >=
258 best_count_shared_peaks)
259 {
260 best_count_shared_peaks =
261 test_peptide_model_cumulating_residual_mass_delta.getCountSharedPeaks();
262 better_peptide_model_cumulating_residual_mass_delta.copyDeep(
263 test_peptide_model_cumulating_residual_mass_delta);
264 }
265 }
266
267 if(better_peptide_model_cumulating_residual_mass_delta.size() > 0)
268 {
269 m_betterPeptideModel.copyDeep(better_peptide_model_cumulating_residual_mass_delta);
270 }
271}

References pappso::specglob::PeptideModel::copyDeep(), pappso::specglob::PeptideModel::getCountSharedPeaks(), m_betterPeptideModel, m_precision, and pappso::specglob::PeptideModel::matchExperimentalPeaks().

Referenced by findBetterPeptideModel().

◆ tryToRemoveOffsets()

void pappso::specglob::PostTreatment::tryToRemoveOffsets ( )
private

try to remove offset (mass difference)

for each mass difference position, count matched peaks and compare to the previous solution. Removes mass difference if it does not degrade the number of matched peaks

Definition at line 201 of file posttreatment.cpp.

202{
203
204 // We'll try to evaluate for each deltaM if it can be a neutral loss or not
205 // For this, we compare the number of shared peaks with and without the shift
206
207 PeptideModel better_peptide_model_for_neutral_loss;
208 std::size_t best_count_shared_peaks = m_betterPeptideModel.getCountSharedPeaks();
209 qDebug() << best_count_shared_peaks;
210 for(std::size_t i = 0; i < m_betterPeptideModel.size(); i++)
211 {
212 if(m_betterPeptideModel.at(i).remove == true)
213 continue;
214 if(m_betterPeptideModel.at(i).mass_difference == 0.0)
215 continue;
216
217
218 // try in the case we remove the offset
219 PeptideModel test_peptide_model_for_neutral_loss = m_betterPeptideModel;
220 test_peptide_model_for_neutral_loss.at(i).mass_difference = 0;
221 test_peptide_model_for_neutral_loss.matchExperimentalPeaks(m_precision);
222
223 qDebug() << test_peptide_model_for_neutral_loss.toString() << " "
224 << test_peptide_model_for_neutral_loss.getCountSharedPeaks() << " "
225 << best_count_shared_peaks;
226 if(test_peptide_model_for_neutral_loss.getCountSharedPeaks() >= best_count_shared_peaks)
227 {
228 best_count_shared_peaks = test_peptide_model_for_neutral_loss.getCountSharedPeaks();
229 better_peptide_model_for_neutral_loss.copyDeep(test_peptide_model_for_neutral_loss);
230 }
231 }
232
233 if(better_peptide_model_for_neutral_loss.size() > 0)
234 {
235 m_betterPeptideModel.copyDeep(better_peptide_model_for_neutral_loss);
236 }
237}

References pappso::specglob::PeptideModel::copyDeep(), pappso::specglob::PeptideModel::getCountSharedPeaks(), m_betterPeptideModel, m_precision, pappso::specglob::PeptideModel::matchExperimentalPeaks(), and pappso::specglob::PeptideModel::toString().

Referenced by findBetterPeptideModel().

Member Data Documentation

◆ m_betterPeptideModel

PeptideModel pappso::specglob::PostTreatment::m_betterPeptideModel
private

Definition at line 113 of file posttreatment.h.

Referenced by PostTreatment(), findBetterPeptideModel(), findReplaceMutations(), getBetterPeptideModel(), tryBetterPositionOffsets(), tryToCumulateOffSets(), and tryToRemoveOffsets().

◆ m_originalPeptideModel

PeptideModel pappso::specglob::PostTreatment::m_originalPeptideModel
private

Definition at line 112 of file posttreatment.h.

Referenced by PostTreatment(), findBetterPeptideModel(), and getOriginalPeptideModel().

◆ m_precision

pappso::PrecisionPtr pappso::specglob::PostTreatment::m_precision
private

Definition at line 114 of file posttreatment.h.

Referenced by PostTreatment(), findBetterPeptideModel(), findReplaceMutations(), tryBetterPositionOffsets(), tryToCumulateOffSets(), and tryToRemoveOffsets().

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