libpappsomspp
Library for mass spectrometry
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peptidefragmention.cpp
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1/**
2 * \file pappsomspp/peptide/peptidefragmention.cpp
3 * \date 10/3/2015
4 * \author Olivier Langella
5 * \brief peptide ion model
6 */
7
8/*******************************************************************************
9 * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
10 *
11 * This file is part of the PAPPSOms++ library.
12 *
13 * PAPPSOms++ is free software: you can redistribute it and/or modify
14 * it under the terms of the GNU General Public License as published by
15 * the Free Software Foundation, either version 3 of the License, or
16 * (at your option) any later version.
17 *
18 * PAPPSOms++ is distributed in the hope that it will be useful,
19 * but WITHOUT ANY WARRANTY; without even the implied warranty of
20 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21 * GNU General Public License for more details.
22 *
23 * You should have received a copy of the GNU General Public License
24 * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
25 *
26 * Contributors:
27 * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
28 *implementation
29 ******************************************************************************/
30
31#include <QDebug>
32#include "peptidefragmention.h"
33#include "pappsomspp/core/pappsoexception.h"
34#include "peptidenaturalisotopelist.h"
35#include "peptiderawfragmentmasses.h"
36
37namespace pappso
38{
39PeptideFragmentIon::PeptideFragmentIon(const PeptideFragmentSp &sp_fragment,
40 Enums::PeptideIon ion_type)
41 : PeptideFragmentIon(sp_fragment, ion_type, 0)
42{
43}
44
45PeptideFragmentIon::PeptideFragmentIon(
46 const PeptideFragmentSp &sp_fragment,
47 Enums::PeptideIon ion_type,
48 unsigned int number_of_neutral_phospho_loss)
49 : msp_fragment(sp_fragment), m_ionType(ion_type)
50{
51 m_mass = msp_fragment.get()->getMass();
52 PeptideDirection direction = msp_fragment.get()->getPeptideIonDirection();
53 if(direction != pappso::getPeptideIonDirection(m_ionType))
54 {
55 throw PappsoException(
56 QString("Enums::PeptideIon %1 is not an %2 fragment")
57 .arg(PeptideFragmentIon::getPeptideIonName(m_ionType))
58 .arg(PeptideFragment::getPeptideIonDirectionName(direction)));
59 }
60 m_mass -= MASSH2O;
61 switch(m_ionType)
62 {
63 // -MASSH2O
64 case Enums::PeptideIon::yp:
65 m_neutralPhosphoLossNumber = number_of_neutral_phospho_loss;
66 m_mass -=
67 ((MASSH2O + MASSPHOSPHORYLATEDR) * m_neutralPhosphoLossNumber);
68 ion_type = Enums::PeptideIon::y;
69 break;
70 case Enums::PeptideIon::bp:
71 m_neutralPhosphoLossNumber = number_of_neutral_phospho_loss;
72 m_mass -=
73 ((MASSH2O + MASSPHOSPHORYLATEDR) * m_neutralPhosphoLossNumber);
74 ion_type = Enums::PeptideIon::b;
75 break;
76 default:
77 break;
78 }
79 m_mass += PeptideRawFragmentMasses::getDeltaMass(ion_type);
80}
81
87
88
89PeptideFragmentIon::PeptideFragmentIon(
90 PeptideFragmentIon &&toCopy) // move constructor
91 : msp_fragment(std::move(toCopy.msp_fragment)),
92 m_ionType(toCopy.m_ionType),
93 m_mass(toCopy.m_mass)
94{
95}
96
100
101
102PeptideDirection
107
108
109const QString
110PeptideFragmentIon::getCompletePeptideIonName(unsigned int charge) const
111{
112
113 std::size_t size = msp_fragment.get()->size();
114 QString plusstr = "+";
115 plusstr = plusstr.repeated(charge);
116 if(m_ionType == Enums::PeptideIon::yp)
117 {
118 return QString("y%1(-P%2)%3")
119 .arg(size)
120 .arg(m_neutralPhosphoLossNumber)
121 .arg(plusstr);
122 }
123 else if(m_ionType == Enums::PeptideIon::bp)
124 {
125 return QString("b%1(-P%2)%3")
126 .arg(size)
127 .arg(m_neutralPhosphoLossNumber)
128 .arg(plusstr);
129 }
130
131 return QString("%1%2%3")
132 .arg(getPeptideIonName(m_ionType))
133 .arg(size)
134 .arg(plusstr);
135}
136
137const QString
138PeptideFragmentIon::getPeptideIonName() const
139{
140 if((m_ionType == Enums::PeptideIon::yp) || (m_ionType == Enums::PeptideIon::bp))
141 {
142 return QString("%1(%2)")
143 .arg(getPeptideIonName(m_ionType))
144 .arg(m_neutralPhosphoLossNumber);
145 }
146 return getPeptideIonName(m_ionType);
147}
148
149const QString
150PeptideFragmentIon::getPeptideIonName(Enums::PeptideIon m_ionType)
151{
152 switch(m_ionType)
153 {
154 case Enums::PeptideIon::y:
155 return "y";
156 break;
157 case Enums::PeptideIon::yp:
158 return "yP";
159 break;
160 case Enums::PeptideIon::ystar:
161 return "y*";
162 break;
163 case Enums::PeptideIon::yo:
164 return "yO";
165 break;
166 case Enums::PeptideIon::bstar:
167 return "b*";
168 break;
169 case Enums::PeptideIon::bo:
170 return "bO";
171 break;
172 case Enums::PeptideIon::a:
173 return "a";
174 break;
175 case Enums::PeptideIon::astar:
176 return "a*";
177 break;
178 case Enums::PeptideIon::ao:
179 return "aO";
180 break;
181 case Enums::PeptideIon::c:
182 return "c";
183 break;
184 // SvgIon.moxygen - mN
185 case Enums::PeptideIon::z:
186 return "z";
187 break;
188 case Enums::PeptideIon::b:
189 return "b";
190 break;
191 case Enums::PeptideIon::bp:
192 return "bP";
193 break;
194 case Enums::PeptideIon::x:
195 return "x";
196 break;
197 default:
198 throw PappsoException(QString("Enums::PeptideIon name not implemented"));
199 break;
200 }
201}
202
203const QColor
204PeptideFragmentIon::getPeptideIonColor(Enums::PeptideIon m_ionType)
205{
206 switch(m_ionType)
207 {
208 case Enums::PeptideIon::y:
209 return QColor("red");
210 break;
211 case Enums::PeptideIon::yp:
212 return QColor("red");
213 break;
214 case Enums::PeptideIon::ystar:
215 return QColor("red");
216 break;
217 case Enums::PeptideIon::yo:
218 return QColor("orange");
219 break;
220 case Enums::PeptideIon::x:
221 return QColor("orange");
222 break;
223 case Enums::PeptideIon::bstar:
224 return QColor("blue");
225 break;
226 case Enums::PeptideIon::bo:
227 return QColor("#ff00ff");
228 break;
229 case Enums::PeptideIon::a:
230 return QColor("green");
231 break;
232 case Enums::PeptideIon::astar:
233 return QColor("green");
234 break;
235 case Enums::PeptideIon::ao:
236 return QColor("green");
237 break;
238 case Enums::PeptideIon::c:
239 return QColor("blue");
240 break;
241 // SvgIon.moxygen - mN
242 case Enums::PeptideIon::z:
243 return QColor("red");
244 break;
245 case Enums::PeptideIon::b:
246 return QColor("blue");
247 break;
248 case Enums::PeptideIon::bp:
249 return QColor("blue");
250 break;
251 default:
252 throw PappsoException(QString("Enums::PeptideIon color not implemented %1")
253 .arg(getPeptideIonName(m_ionType)));
254 break;
255 }
256}
257
258int
259PeptideFragmentIon::getNumberOfAtom(Enums::AtomIsotopeSurvey atom) const
260{
261 int number = msp_fragment.get()->getNumberOfAtom(atom);
262 int diff = 0;
263 switch(atom)
264 {
265 case Enums::AtomIsotopeSurvey::C:
266 switch(m_ionType)
267 {
268 case Enums::PeptideIon::y:
269 break;
270 case Enums::PeptideIon::yp:
271 // H 1 O 3 P 1 + H 2 0
272 break;
273 case Enums::PeptideIon::ystar:
274 // m_mass -= MASSNH3;
275 break;
276 case Enums::PeptideIon::yo:
277 // m_mass -= MASSH2O;
278 break;
279 case Enums::PeptideIon::bstar:
280 // m_mass -= MASSH2O;
281 // m_mass -= MASSNH3;
282 break;
283 case Enums::PeptideIon::bo:
284 // m_mass -= MASSH2O;
285 // m_mass -= MASSH2O;
286 break;
287 case Enums::PeptideIon::a:
288 // m_mass -= MASSH2O;
289 // m_mass -= MASSCO;
290 diff = -1;
291 break;
292 case Enums::PeptideIon::c:
293 // m_mass += MASSNH3;
294 break;
295 // SvgIon.moxygen - mN
296 case Enums::PeptideIon::z:
297 // m_mass -= MASSH2O;
298 // m_mass += MASSOXYGEN - MASSNITROGEN - MPROTIUM;
299 break;
300 case Enums::PeptideIon::b:
301 // m_mass -= MASSH2O;
302 break;
303 case Enums::PeptideIon::bp:
304 // H 1 O 3 P 1 + H 2 0
305 break;
306
307 case Enums::PeptideIon::astar:
308 // m_mass -= MASSH2O;
309 // m_mass = - MASSCO - MASSNH3;
310 diff = -1;
311 break;
312 case Enums::PeptideIon::ao:
313 // m_mass -= MASSH2O;
314 // m_mass = - MASSCO - MASSH2O;
315 diff = -1;
316 break;
317 case Enums::PeptideIon::x:
318 // +MASSCO + MASSOXYGEN
319 diff = +1;
320 break;
321 default:
322 throw PappsoException(QString("Enums::PeptideIon name not implemented"));
323 break;
324 }
325 break;
326 case Enums::AtomIsotopeSurvey::H:
327 switch(m_ionType)
328 {
329 case Enums::PeptideIon::y:
330 break;
331 case Enums::PeptideIon::yp:
332 // H 1 O 3 P 1 + H 2 0
333 diff = -3 * m_neutralPhosphoLossNumber;
334 break;
335 case Enums::PeptideIon::ystar:
336 // m_mass -= MASSNH3;
337 diff = -3;
338 break;
339 case Enums::PeptideIon::yo:
340 // m_mass -= MASSH2O;
341 diff = -2;
342 break;
343 case Enums::PeptideIon::bstar:
344 // m_mass -= MASSH2O;
345 // m_mass -= MASSNH3;
346 diff = -5;
347 break;
348 case Enums::PeptideIon::bo:
349 // m_mass -= MASSH2O;
350 // m_mass -= MASSH2O;
351 diff = -4;
352 break;
353 case Enums::PeptideIon::a:
354 // m_mass -= MASSH2O;
355 // m_mass -= MASSCO;
356 diff = -2;
357 break;
358 case Enums::PeptideIon::c:
359 // m_mass += MASSNH3;
360 diff = -3;
361 break;
362 // SvgIon.moxygen - mN
363 case Enums::PeptideIon::z:
364 // m_mass -= MASSH2O;
365 // m_mass += MASSOXYGEN - MASSNITROGEN - MPROTIUM;
366 diff = -3;
367 break;
368 case Enums::PeptideIon::b:
369 // m_mass -= MASSH2O;
370 diff = -2;
371 break;
372 case Enums::PeptideIon::bp:
373 // H 1 O 3 P 1 + H 2 0
374 diff = -3 * m_neutralPhosphoLossNumber;
375 break;
376
377
378 case Enums::PeptideIon::astar:
379 // m_mass -= MASSH2O;
380 // m_mass = - MASSCO - MASSNH3;
381 diff = -5;
382 break;
383 case Enums::PeptideIon::ao:
384 // m_mass -= MASSH2O;
385 // m_mass = - MASSCO - MASSH2O;
386 diff = -4;
387 break;
388 case Enums::PeptideIon::x:
389 // +MASSCO + MASSOXYGEN
390 diff = -2;
391 break;
392 default:
393 throw PappsoException(QString("Enums::PeptideIon name not implemented"));
394 break;
395 }
396 break;
397 case Enums::AtomIsotopeSurvey::N:
398 switch(m_ionType)
399 {
400 case Enums::PeptideIon::y:
401 break;
402 case Enums::PeptideIon::yp:
403 // H 1 O 3 P 1 + H 2 0
404 break;
405
406 case Enums::PeptideIon::ystar:
407 // m_mass -= MASSNH3;
408 diff = -1;
409 break;
410 case Enums::PeptideIon::yo:
411 // m_mass -= MASSH2O;
412 break;
413 case Enums::PeptideIon::bstar:
414 // m_mass -= MASSH2O;
415 // m_mass -= MASSNH3;
416 diff = -1;
417 break;
418 case Enums::PeptideIon::bo:
419 // m_mass -= MASSH2O;
420 // m_mass -= MASSH2O;
421 break;
422 case Enums::PeptideIon::a:
423 // m_mass -= MASSH2O;
424 // m_mass -= MASSCO;
425 break;
426 case Enums::PeptideIon::c:
427 // m_mass += MASSNH3;
428 diff = -1;
429 break;
430 // SvgIon.moxygen - mN
431 case Enums::PeptideIon::z:
432 // m_mass -= MASSH2O;
433 // m_mass += MASSOXYGEN - MASSNITROGEN - MPROTIUM;
434 diff = -1;
435 break;
436 case Enums::PeptideIon::b:
437 // m_mass -= MASSH2O;
438 break;
439 case Enums::PeptideIon::bp:
440 // H 1 O 3 P 1 + H 2 0
441 break;
442
443
444 case Enums::PeptideIon::astar:
445 // m_mass -= MASSH2O;
446 // m_mass = - MASSCO - MASSNH3;
447 diff = -1;
448 break;
449 case Enums::PeptideIon::ao:
450 // m_mass -= MASSH2O;
451 // m_mass = - MASSCO - MASSH2O;
452 break;
453 case Enums::PeptideIon::x:
454 // +MASSCO + MASSOXYGEN
455 break;
456 default:
457 throw PappsoException(QString("Enums::PeptideIon name not implemented"));
458 break;
459 }
460 break;
461 case Enums::AtomIsotopeSurvey::O:
462 switch(m_ionType)
463 {
464 case Enums::PeptideIon::y:
465 break;
466 case Enums::PeptideIon::yp:
467 // H 1 O 3 P 1 + H 2 0
468 diff = -4 * m_neutralPhosphoLossNumber;
469 break;
470
471 case Enums::PeptideIon::ystar:
472 // m_mass -= MASSNH3;
473 break;
474 case Enums::PeptideIon::yo:
475 // m_mass -= MASSH2O;
476 diff = -1;
477 break;
478 case Enums::PeptideIon::bstar:
479 // m_mass -= MASSH2O;
480 // m_mass -= MASSNH3;
481 diff = -1;
482 break;
483 case Enums::PeptideIon::bo:
484 // m_mass -= MASSH2O;
485 // m_mass -= MASSH2O;
486 diff = -2;
487 break;
488 case Enums::PeptideIon::a:
489 // m_mass -= MASSH2O;
490 // m_mass -= MASSCO;
491 diff = -2;
492 break;
493 case Enums::PeptideIon::c:
494 // m_mass += MASSNH3;
495 break;
496 // SvgIon.moxygen - mN
497 case Enums::PeptideIon::z:
498 // m_mass -= MASSH2O;
499 // m_mass += MASSOXYGEN - MASSNITROGEN - MPROTIUM;
500 diff = -2;
501 break;
502 case Enums::PeptideIon::b:
503 // m_mass -= MASSH2O;
504 diff = -1;
505 break;
506 case Enums::PeptideIon::bp:
507 // H 1 O 3 P 1 + H 2 0
508 diff = -4 * m_neutralPhosphoLossNumber;
509 break;
510
511
512 case Enums::PeptideIon::astar:
513 // m_mass -= MASSH2O;
514 // m_mass = - MASSCO - MASSNH3;
515 diff = -2;
516 break;
517 case Enums::PeptideIon::ao:
518 // m_mass -= MASSH2O;
519 // m_mass = - MASSCO - MASSH2O;
520 diff = -3;
521 break;
522 case Enums::PeptideIon::x:
523 // +MASSCO + MASSOXYGEN
524 diff = +1;
525 break;
526 default:
527 throw PappsoException(
528 QObject::tr("Enums::PeptideIon name not implemented"));
529 break;
530 }
531 break;
532 case Enums::AtomIsotopeSurvey::S:
533 break;
534 default:
535 qDebug() << "PeptideFragmentIon::getNumberOfAtom(Enums::AtomIsotopeSurvey "
536 "atom) NOT IMPLEMENTED";
537 }
538 return number + diff;
539}
540
541
542int
543PeptideFragmentIon::getNumberOfIsotope(Enums::Isotope isotope) const
544{
545 int number = msp_fragment.get()->getNumberOfIsotope(isotope);
546 return number;
547}
548
549PeptideFragmentIonSp
550PeptideFragmentIon::makePeptideFragmentIonSp() const
551{
552 return std::make_shared<PeptideFragmentIon>(*this);
553}
554
555
556unsigned int
557PeptideFragmentIon::size() const
558{
559 return msp_fragment.get()->size();
560}
561
562const QString
563PeptideFragmentIon::getSequence() const
564{
565 return msp_fragment.get()->getSequence();
566}
567
568const PeptideFragmentSp &
573
574const QString
575PeptideFragmentIon::getName() const
576{
577 return QString("%1-%2").arg(getPeptideIonName(m_ionType)).arg(size());
578}
579
580pappso_double
581PeptideFragmentIon::getMass() const
582{
583 return m_mass;
584}
585
586Enums::PeptideIon
591PeptideDirection
592PeptideFragmentIon::getPeptideIonDirection() const
593{
594 return msp_fragment.get()->getPeptideIonDirection();
595}
596unsigned int
601
602bool
603PeptideFragmentIon::isPalindrome() const
604{
605 return msp_fragment.get()->isPalindrome();
606}
607
608
609} // namespace pappso
pappso::PeptideFragmentIon::makePeptideFragmentIonSp
PeptideFragmentIonSp makePeptideFragmentIonSp() const
Definition peptidefragmention.cpp:550
pappso::PeptideFragmentIon::m_ionType
const Enums::PeptideIon m_ionType
Definition peptidefragmention.h:96
pappso::PeptideFragmentIon::getPeptideIonType
Enums::PeptideIon getPeptideIonType() const
Definition peptidefragmention.cpp:587
pappso::PeptideFragmentIon::getPeptideIonName
const QString getPeptideIonName() const
Definition peptidefragmention.cpp:138
pappso::PeptideFragmentIon::getNumberOfAtom
virtual int getNumberOfAtom(Enums::AtomIsotopeSurvey atom) const override
get the number of atom C, O, N, H in the molecule
Definition peptidefragmention.cpp:259
pappso::PeptideFragmentIon::getPeptideFragmentSp
virtual const PeptideFragmentSp & getPeptideFragmentSp() const
Definition peptidefragmention.cpp:569
pappso::PeptideFragmentIon::PeptideFragmentIon
PeptideFragmentIon(const PeptideFragmentSp &sp_fragment, Enums::PeptideIon ion_type, unsigned int number_of_neutral_phospho_loss)
Definition peptidefragmention.cpp:45
pappso::PeptideFragmentIon::msp_fragment
const PeptideFragmentSp msp_fragment
Definition peptidefragmention.h:95
pappso::PeptideFragmentIon::getCompletePeptideIonName
const QString getCompletePeptideIonName(unsigned int charge) const
get a complete ion name string
Definition peptidefragmention.cpp:110
pappso::PeptideFragmentIon::getNumberOfNeutralPhosphoLoss
unsigned int getNumberOfNeutralPhosphoLoss() const
Definition peptidefragmention.cpp:597
pappso::PeptideFragmentIon::getSequence
virtual const QString getSequence() const override
amino acid sequence without modification
Definition peptidefragmention.cpp:563
pappso::PeptideFragmentIon::size
virtual unsigned int size() const override
Definition peptidefragmention.cpp:557
pappso::PeptideFragmentIon::getNumberOfIsotope
virtual int getNumberOfIsotope(Enums::Isotope isotope) const override
get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule
Definition peptidefragmention.cpp:543
pappso::PeptideFragmentIon::getMass
pappso_double getMass() const override
Definition peptidefragmention.cpp:581
pappso::PeptideFragmentIon::getPeptideIonColor
static const QColor getPeptideIonColor(Enums::PeptideIon ion_type)
Definition peptidefragmention.cpp:204
pappso::PeptideFragmentIon::getPeptideIonDirection
PeptideDirection getPeptideIonDirection() const
Definition peptidefragmention.cpp:592
pappso::PeptideFragmentIon::isPalindrome
virtual bool isPalindrome() const override
tells if the peptide sequence is a palindrome
Definition peptidefragmention.cpp:603
pappso::PeptideFragmentIon::getName
virtual const QString getName() const override
Definition peptidefragmention.cpp:575
pappso::PeptideFragment::getPeptideIonDirectionName
static const QString getPeptideIonDirectionName(PeptideDirection direction)
Definition peptidefragment.cpp:103
pappso::PeptideRawFragmentMasses::getDeltaMass
static pappso_double getDeltaMass(Enums::PeptideIon ion_type)
Definition peptiderawfragmentmasses.cpp:56
pappso::Enums::PeptideIon
PeptideIon
Enums::PeptideIon enum defines all types of ions (Nter or Cter)
Definition types.h:286
pappso::Enums::PeptideIon::a
@ a
Nter aldimine ions.
Definition types.h:290
pappso::Enums::PeptideIon::y
@ y
Cter amino ions.
Definition types.h:295
pappso::Enums::PeptideIon::c
@ c
Nter amino ions.
Definition types.h:294
pappso::Enums::PeptideIon::astar
@ astar
Nter aldimine ions + NH3 loss.
Definition types.h:291
pappso::Enums::PeptideIon::ystar
@ ystar
Cter amino ions + NH3 loss.
Definition types.h:296
pappso::Enums::PeptideIon::yo
@ yo
Cter amino ions + H2O loss.
Definition types.h:297
pappso::Enums::PeptideIon::bstar
@ bstar
Nter acylium ions + NH3 loss.
Definition types.h:288
pappso::Enums::PeptideIon::b
@ b
Nter acylium ions.
Definition types.h:287
pappso::Enums::PeptideIon::x
@ x
Cter acylium ions.
Definition types.h:300
pappso::Enums::PeptideIon::bo
@ bo
Nter acylium ions + H2O loss.
Definition types.h:289
pappso::Enums::PeptideIon::ao
@ ao
Nter aldimine ions + H2O loss.
Definition types.h:292
pappso::Enums::PeptideIon::z
@ z
Cter carbocations.
Definition types.h:298
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
pappso::PeptideFragmentIonSp
std::shared_ptr< const PeptideFragmentIon > PeptideFragmentIonSp
Definition peptidefragmention.h:46
pappso::PeptideDirection
PeptideDirection
Definition peptide.h:46
pappso::pappso_double
double pappso_double
A type definition for doubles.
Definition types.h:61
pappso::getPeptideIonDirection
PeptideDirection getPeptideIonDirection(Enums::PeptideIon ion_type)
get the direction of a peptide ion
Definition peptide.cpp:95
pappso::MASSH2O
const pappso_double MASSH2O((MPROTIUM *2)+MASSOXYGEN)
pappso::MASSPHOSPHORYLATEDR
const pappso_double MASSPHOSPHORYLATEDR(MPROTIUM+(MASSOXYGEN *3)+MASSPHOSPHORUS)
pappso::PeptideFragmentSp
std::shared_ptr< const PeptideFragment > PeptideFragmentSp
Definition peptidefragment.h:45