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
36namespace pappso
37{
38/************ Typedefs **************************************************/
39
40/** \var typedef QString PeptideStr
41 \brief A type definition for PeptideStr
42 */
43typedef QString PeptideStr;
44
45/** \var typedef double pappso_double
46 \brief A type definition for doubles
47 */
48typedef double pappso_double;
49
50/** \var typedef float mcq_float
51 \brief A type definition for floats
52 */
53typedef float pappso_float;
54
55typedef unsigned int uint;
56
57/*********** enumerations *********************************/
58
59/** \def PrecisionUnit ppm or dalton
60 *
61 */
62enum 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 */
75enum 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 */
90enum 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 */
106enum 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,
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 */
132enum 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 */
162enum class DataCompression : std::int8_t
163{
164 unset = -1, ///< not net
165 none = 0, ///< no compression
166 zlib = 1, ///< zlib compresssion
167};
168
169
170enum 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
179enum class Axis : std::int8_t
180{
181 unset = 0x000,
182 x = 1 << 0,
183 y = 1 << 1,
184 z = 1 << 2,
185};
186
187
188enum 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 */
199enum 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 */
213const pappso_double MHPLUS(1.007276466879);
214const 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 */
223const pappso_double MPROTIUM(1.007825032241);
224
225
226/** \def ONEMILLION 1000000
227 \brief One million integer, why not.
228 */
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
256const pappso_double MASSOXYGEN(15.99491461956);
259const pappso_double MASSNITROGEN(14.0030740048);
262const pappso_double MASSPHOSPHORUS(30.973761998);
263const 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
270const 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 */
278const 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 */
285const 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 */
291const 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 */
297const 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 */
304const 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 */
311
312/** \def DIFFO16O17
313 \brief The (monoisotopic) mass difference between O16 and O17 stable isotope of
314 oxygen
315 */
317
318/** \def DIFFN14N15
319 \brief The (monoisotopic) mass difference between N14 and N15 stable isotope of
320 nitrogen
321 */
322const 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 */
329const 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 0.98921194185046687152862432412803173065185546875000000000000000);
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 */
384enum 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)
const pappso_double ABUNDANCEC12(0.98921194185046687152862432412803173065185546875000000000000000)
PeptideIon
PeptideIon enum defines all types of ions (Nter or Cter)
Definition: types.h:385
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
@ 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
@ 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 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)