libpappsomspp
Library for mass spectrometry
types.h
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1 /**
2  * \file pappsomspp/types.h
3  * \date 4/3/2015
4  * \author Olivier Langella
5  * \brief This header contains all the type re-definitions and all
6  * the global variables definitions used in the PAPPSOms++ library.
7  */
8 
9 /*******************************************************************************
10  * Copyright (c) 2015 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 
32 #pragma once
33 
34 #include <QString>
35 
36 namespace pappso
37 {
38 /************ Typedefs **************************************************/
39 
40 /** \var typedef QString PeptideStr
41  \brief A type definition for PeptideStr
42  */
43 typedef QString PeptideStr;
44 
45 /** \var typedef double pappso_double
46  \brief A type definition for doubles
47  */
48 typedef double pappso_double;
49 
50 /** \var typedef float mcq_float
51  \brief A type definition for floats
52  */
53 typedef float pappso_float;
54 
55 typedef unsigned int uint;
56 
57 /*********** enumerations *********************************/
58 
59 /** \def PrecisionUnit ppm or dalton
60  *
61  */
62 enum class PrecisionUnit
63 {
64  none,
65  dalton,
66  ppm,
67  res,
68  mz,
69  last
70 };
71 
72 /** \def AtomIsotopeSurvey list of atoms on which isotopes may occurs
73  *
74  */
75 enum class AtomIsotopeSurvey : std::int8_t
76 {
77  C,
78  H,
79  O,
80  N,
81  S,
82  last
83 };
84 
85 
86 /** \def Isotope list of isotopes taken into account for peptide abundance
87  * calculation
88  *
89  */
90 enum class Isotope
91 {
92  C13,
93  H2,
94  O17,
95  O18,
96  N15,
97  S33,
98  S34,
99  S36
100 };
101 
102 
103 /** \def MzFormat mz data file format types
104  *
105  */
106 enum class MzFormat : std::int8_t
107 {
108  unknown = 0, ///< unknown format
109  mzML = 1, ///< mzML
110  mzXML = 2, ///< mzXML
111  MGF = 3, ///< Mascot format
112  SQLite3 = 4, ///< SQLite3 format
113  xy = 5, ///< (x,y) format
114  mz5 = 6, //< MZ5 format
115  msn = 7, //< MS_MS2 format
116  abSciexWiff = 8,
117  abSciexT2D = 9,
118  agilentMassHunter = 10,
119  thermoRaw = 11,
120  watersRaw = 12,
121  brukerFid = 13,
122  brukerYep = 14,
123  brukerBaf = 15,
124  brukerTims = 16,
125  last = 17
126 };
127 
128 
129 /** \def MzFormat mz data file format types
130  *
131  */
132 enum class AminoAcidChar : char
133 {
134  alanine = 'A',
135  cysteine = 'C',
136  aspartic_acid = 'D',
137  glutamic_acid = 'E',
138  phenylalanine = 'F',
139  glycine = 'G',
140  histidine = 'H',
141  isoleucine = 'I',
142  lysine = 'K',
143  leucine = 'L',
144  methionine = 'M',
145  asparagine = 'N',
146  proline = 'P',
147  glutamine = 'Q',
148  arginine = 'R',
149  serine = 'S',
150  threonine = 'T',
151  valine = 'V',
152  tryptophan = 'W',
153  tyrosine = 'Y',
154  selenocysteine = 'U',
155  pyrrolysine = 'O',
156 };
157 
158 
159 /** \def Data compression types
160  *
161  */
162 enum class DataCompression : std::int8_t
163 {
164  unset = -1, ///< not net
165  none = 0, ///< no compression
166  zlib = 1, ///< zlib compresssion
167 };
168 
169 
170 enum class DataKind : std::int8_t
171 {
172  unset = -1, ///< not set
173  rt = 0, ///< Retention time
174  dt = 1, ///< Drift time
175  mz = 2, ///< m/z
176 };
177 
178 
179 enum class Axis : std::int8_t
180 {
181  unset = 0x000,
182  x = 1 << 0,
183  y = 1 << 1,
184  z = 1 << 2,
185 };
186 
187 
188 enum class AxisScale : std::int8_t
189 {
190  unset = 0,
191  orig = 1,
192  log10 = 2,
193 };
194 
195 
196 /** \def XixExtactMethod method to extract Xic
197  *
198  */
199 enum class XicExtractMethod : std::int8_t
200 {
201  sum = 1, ///< sum of intensities
202  max = 2 ///< maximum of intensities
203 };
204 
205 
206 /*********** Global variables definitions*********************************/
207 
208 /** \def MHPLUS 1.007276466879
209  \brief The (monoisotopic) mass of the H+ ion
210  https://en.wikipedia.org/wiki/Proton (One Proton alone)
211  1.007276466879
212  */
213 const pappso_double MHPLUS(1.007276466879);
214 const pappso_double MPROTON(1.007276466879);
215 
216 /** \def MPROTIUM 1.00782503207
217  \brief The (monoisotopic) mass of the H atom
218  https://en.wikipedia.org/wiki/Isotopes_of_hydrogen (One proton + One electron)
219  1.00782503207
220 
221  Note that as of 20191028, that same page says: 1.007825032241
222  */
223 const pappso_double MPROTIUM(1.007825032241);
224 
225 
226 /** \def ONEMILLION 1000000
227  \brief One million integer, why not.
228  */
229 const pappso_double ONEMILLION(1000000);
230 
231 
232 /** @file
233  * https://forgemia.inra.fr/pappso/massxpert/-/blob/be60e53480f68d36afa95c809cffd68d4fb46c79/data/polChemDefs/protein-1-letter-libisospec-atomic-data/protein-1-letter-libisospec-atomic-data.xml
234  * abundance of sulfur extracted from 'massXpert' polymer definitions
235  */
236 // <name>Sulfur</name>
237 // <symbol>S</symbol>
238 // <isotope>
239 // <mass>31.9720711741</mass>
240 // <abund>94.985001199904004920426814351230859756469726562500000000000000</abund>
241 // </isotope>
242 // <isotope>
243 // <mass>32.9714589101</mass>
244 // <abund>0.751939844812414937003097747947322204709053039550781250000000</abund>
245 // </isotope>
246 // <isotope>
247 // <mass>33.9678670300</mass>
248 // <abund>4.252059835213182203972337447339668869972229003906250000000000</abund>
249 // </isotope>
250 // <isotope>
251 // <mass>35.9670812000</mass>
252 // <abund>0.010999120070394368536836893213148869108408689498901367187500</abund>
253 // </isotope>
254 
255 
256 const pappso_double MASSOXYGEN(15.99491461956);
259 const pappso_double MASSNITROGEN(14.0030740048);
262 const pappso_double MASSPHOSPHORUS(30.973761998);
263 const pappso_double MASSSULFUR(31.9720711741);
264 
265 // id: MOD:00696 name: phosphorylated residue H 1 O 3 P 1
268 
269 // Selenium : warning lot of isotopes
270 const pappso_double MASSSELENIUM(79.916520); // 79.916520 //78.971
271 
272 // CHNOS
273 
274 /** \def DIFFC12C13 1.0033548378
275  \brief The (monoisotopic) mass difference between C12 (12u) and C13 stable
276  isotope of carbon
277  */
278 const pappso_double DIFFC12C13(1.0033548378);
279 
280 /** \def DIFFS32S33 0.99938776
281  \brief The (monoisotopic) mass difference between S32 (31.97207100u) and S33
282  (32.97145876u) stable isotope of sulfur
283  https://en.wikipedia.org/wiki/Isotopes_of_sulfur
284  */
285 const pappso_double DIFFS32S33(32.9714589101 - MASSSULFUR);
286 
287 /** \def DIFFS32S34 1.9957959
288  \brief The (monoisotopic) mass difference between S32 (31.97207100u) and S34
289  (33.96786690u) stable isotope of sulfur
290  */
291 const pappso_double DIFFS32S34(33.9678670300 - MASSSULFUR);
292 
293 /** \def DIFFS32S36 3.99500976
294  \brief The (monoisotopic) mass difference between S32 (31.97207100u) and S36
295  (35.96708076u) stable isotope of sulfur
296  */
297 const pappso_double DIFFS32S36(35.9670812000 - MASSSULFUR);
298 
299 
300 /** \def DIFFH1H2
301  \brief The (monoisotopic) mass difference between H1 and H2 stable isotope of
302  hydrogen
303  */
304 const pappso_double DIFFH1H2(2.0141017778 - MPROTIUM);
305 
306 /** \def DIFFO16O18
307  \brief The (monoisotopic) mass difference between O16 and O18 stable isotope of
308  oxygen
309  */
310 const pappso_double DIFFO16O18(17.9991610 - MASSOXYGEN);
311 
312 /** \def DIFFO16O17
313  \brief The (monoisotopic) mass difference between O16 and O17 stable isotope of
314  oxygen
315  */
316 const pappso_double DIFFO16O17(16.99913150 - MASSOXYGEN);
317 
318 /** \def DIFFN14N15
319  \brief The (monoisotopic) mass difference between N14 and N15 stable isotope of
320  nitrogen
321  */
322 const pappso_double DIFFN14N15(15.0001088982 - MASSNITROGEN);
323 
324 
325 // http://education.expasy.org/student_projects/isotopident/htdocs/motza.html
326 /** \def ABUNDANCEH2 0.0156%
327  \brief H2 isotope abundance
328  */
329 const pappso_double
330  ABUNDANCEH2(0.00011570983569203332000374651045149221317842602729797363281250);
331 
332 /** \def ABUNDANCEN15 0.00364
333  \brief N15 isotope abundance
334  */
336  0.00364198543205827118818262988497735932469367980957031250000000);
337 
338 /** \def ABUNDANCEO17
339  \brief O17 isotope abundance
340  */
342  0.00038099847600609595965615028489992255344986915588378906250000);
343 
344 /** \def ABUNDANCEO18 0.2%
345  \brief O18 isotope abundance
346  */
348  0.00205139179443282221315669744399201590567827224731445312500000);
349 
350 /** \def ABUNDANCEC13 1.109%
351  \brief C13 isotope abundance
352  */
354  0.01078805814953308406245469086570665240287780761718750000000000);
355 
356 /** \def ABUNDANCEC12 98.89%
357  \brief C12 abundance
358  */
360  0.098921194185046687152862432412803173065185546875000000000000000);
361 
362 
363 /** \def ABUNDANCES33 0.00750
364  \brief S33 abundance
365  */
367  0.00751939844812414937003097747947322204709053039550781250000000);
368 
369 /** \def ABUNDANCES34 0.0429
370  \brief S34 abundance
371  */
373  0.04252059835213182203972337447339668869972229003906250000000000);
374 
375 /** \def ABUNDANCES36 0.00020
376  \brief S36 abundance
377  */
379  0.00010999120070394368536836893213148869108408689498901367187500);
380 
381 
382 /** \brief PeptideIon enum defines all types of ions (Nter or Cter)
383  */
384 enum class PeptideIon : std::int8_t
385 {
386  b = 0, ///< Nter acylium ions
387  bstar = 1, ///< Nter acylium ions + NH3 loss
388  bo = 2, ///< Nter acylium ions + H2O loss
389  a = 3, ///< Nter aldimine ions
390  astar = 4, ///< Nter aldimine ions + NH3 loss
391  ao = 5, ///< Nter aldimine ions + H2O loss
392  bp = 6,
393  c = 7, ///< Nter amino ions
394  y = 8, ///< Cter amino ions
395  ystar = 9, ///< Cter amino ions + NH3 loss
396  yo = 10, ///< Cter amino ions + H2O loss
397  z = 11, ///< Cter carbocations
398  yp = 12,
399  x = 13 ///< Cter acylium ions
400 };
401 
402 /** \brief only usefull for inernal usefull
403  * DO not change this value : it is used to define static array size
404  */
405 #define PEPTIDE_ION_TYPE_COUNT 14
406 } // namespace pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
const pappso_double MPROTON(1.007276466879)
PeptideIon
PeptideIon enum defines all types of ions (Nter or Cter)
Definition: types.h:385
@ 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.
AminoAcidChar
Definition: types.h:133
Axis
Definition: types.h:180
const pappso_double DIFFS32S33(32.9714589101 - MASSSULFUR)
PrecisionUnit
Definition: types.h:63
const pappso_double DIFFS32S34(33.9678670300 - MASSSULFUR)
MzFormat
Definition: types.h:107
@ xy
(x,y) format
@ unknown
unknown format
@ SQLite3
SQLite3 format.
@ MGF
Mascot format.
const pappso_double DIFFO16O17(16.99913150 - MASSOXYGEN)
const pappso_double MASSCARBON(12)
const pappso_double MASSPHOSPHORUS(30.973761998)
const pappso_double MASSSULFUR(31.9720711741)
const pappso_double ABUNDANCES36(0.00010999120070394368536836893213148869108408689498901367187500)
QString PeptideStr
A type definition for PeptideStr.
Definition: types.h:43
DataCompression
Definition: types.h:163
@ none
no compression
@ zlib
zlib compresssion
const pappso_double MASSCO(MASSCARBON+MASSOXYGEN)
const pappso_double ONEMILLION(1000000)
const pappso_double ABUNDANCEN15(0.00364198543205827118818262988497735932469367980957031250000000)
const pappso_double DIFFS32S36(35.9670812000 - MASSSULFUR)
const pappso_double MASSSELENIUM(79.916520)
const pappso_double MHPLUS(1.007276466879)
AtomIsotopeSurvey
Definition: types.h:76
double pappso_double
A type definition for doubles.
Definition: types.h:48
Isotope
Definition: types.h:91
AxisScale
Definition: types.h:189
const pappso_double ABUNDANCEC13(0.01078805814953308406245469086570665240287780761718750000000000)
const pappso_double MPROTIUM(1.007825032241)
const pappso_double MASSH2O((MPROTIUM *2)+MASSOXYGEN)
const pappso_double ABUNDANCEO17(0.00038099847600609595965615028489992255344986915588378906250000)
const pappso_double ABUNDANCEH2(0.00011570983569203332000374651045149221317842602729797363281250)
DataKind
Definition: types.h:171
@ dt
Drift time.
@ rt
Retention time.
const pappso_double MASSNH3((MPROTIUM *3)+MASSNITROGEN)
unsigned int uint
Definition: types.h:55
const pappso_double ABUNDANCES34(0.04252059835213182203972337447339668869972229003906250000000000)
const pappso_double MASSNITROGEN(14.0030740048)
const pappso_double MASSOXYGEN(15.99491461956)
const pappso_double MASSPHOSPHORYLATEDR(MPROTIUM+(MASSOXYGEN *3)+MASSPHOSPHORUS)
const pappso_double ABUNDANCEC12(0.098921194185046687152862432412803173065185546875000000000000000)
const pappso_double ABUNDANCEO18(0.00205139179443282221315669744399201590567827224731445312500000)
const pappso_double DIFFO16O18(17.9991610 - MASSOXYGEN)
const pappso_double ABUNDANCES33(0.00751939844812414937003097747947322204709053039550781250000000)
const pappso_double DIFFN14N15(15.0001088982 - MASSNITROGEN)
XicExtractMethod
Definition: types.h:200
@ sum
sum of intensities
@ max
maximum of intensities
const pappso_double DIFFC12C13(1.0033548378)
float pappso_float
Definition: types.h:53
const pappso_double DIFFH1H2(2.0141017778 - MPROTIUM)