-
Notifications
You must be signed in to change notification settings - Fork 4
/
ITraqIntensityCorrection.cs
1267 lines (1088 loc) · 64.5 KB
/
ITraqIntensityCorrection.cs
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
using System;
using MASIC.Data;
namespace MASIC
{
// ReSharper disable CommentTypo
/// <summary>
/// <para>
/// This class corrects the intensities of iTraq or TMT data, based on the expected overlapping isotopic distributions
/// It supports 4-plex and 8-plex iTraq
/// It also supports TMT10, TMT11, TMT16 (aka TMTpro), and TMT18
/// </para>
/// <para>
/// The isotopic distribution weights are provided by the iTraq or TMT manufacturer
/// </para>
/// </summary>
/// <remarks>
/// There are two options for the iTRAQ 4-plex weights:
/// CorrectionFactorsiTRAQ4Plex.ABSciex
/// CorrectionFactorsiTRAQ4Plex.BroadInstitute
/// </remarks>
// ReSharper restore CommentTypo
public class ITraqIntensityCorrection
{
// ReSharper disable CommentTypo
// Ignore Spelling: Biosystems, Da, MASIC, Mertins, Philipp, plex, Proteomics, Sciex, Sickmann, Traq, Vaudel
private const int FOUR_PLEX_MATRIX_LENGTH = 4;
private const int EIGHT_PLEX_HIGH_RES_MATRIX_LENGTH = 8;
private const int EIGHT_PLEX_LOW_RES_MATRIX_LENGTH = 9;
private const int TEN_PLEX_TMT_MATRIX_LENGTH = 10;
private const int ELEVEN_PLEX_TMT_MATRIX_LENGTH = 11;
private const int SIXTEEN_PLEX_TMT_MATRIX_LENGTH = 16;
private const int EIGHTEEN_PLEX_TMT_MATRIX_LENGTH = 18;
private const int THIRTY_TWO_PLEX_TMT_MATRIX_LENGTH = 32;
private const int THIRTY_FIVE_PLEX_TMT_MATRIX_LENGTH = 35;
// ReSharper disable IdentifierTypo
/// <summary>
/// 4-plex iTRAQ correction factor type
/// </summary>
public enum CorrectionFactorsITRAQ4Plex
{
/// <summary>
/// AB Sciex
/// </summary>
ABSciex = 0,
/// <summary>
/// Broad Institute
/// </summary>
/// <remarks>
/// Provided by Philipp Mertins at the Broad Institute (pmertins@broadinstitute.org)
/// </remarks>
BroadInstitute = 1
}
// ReSharper restore IdentifierTypo
// ReSharper restore CommentTypo
private struct IsotopeContributionType
{
public float Minus2;
public float Minus1;
public float Zero;
public float Plus1;
public float Plus2;
public readonly override string ToString()
{
return string.Format("{0:F2} {1:F2} {2:F2} {3:F2} {4:F2}", Minus2, Minus1, Zero, Plus1, Plus2);
}
}
/// <summary>
/// Matrix of coefficients, derived from the isotope contribution table
/// </summary>
// ReSharper disable once IdentifierTypo
private double[,] mCoeffs;
private readonly MatrixDecompositionUtility.LUDecomposition mMatrixUtility;
/// <summary>
/// Reporter ion mode
/// </summary>
public ReporterIons.ReporterIonMassModeConstants ReporterIonMode { get; private set; }
/// <summary>
/// 4-plex iTRAQ correction factor type
/// </summary>
public CorrectionFactorsITRAQ4Plex ITraq4PlexCorrectionFactorType { get; private set; }
/// <summary>
/// Constructor that assumes iTraqCorrectionFactorType = ABSciex
/// </summary>
/// <param name="reporterIonMode">iTRAQ or TMT mode</param>
// ReSharper disable once UnusedMember.Global
public ITraqIntensityCorrection(ReporterIons.ReporterIonMassModeConstants reporterIonMode)
: this(reporterIonMode, CorrectionFactorsITRAQ4Plex.ABSciex)
{
}
/// <summary>
/// Constructor
/// </summary>
/// <remarks>The iTraqCorrectionFactorType parameter is only used if reporterIonMode is ITraqFourMZ</remarks>
/// <param name="reporterIonMode">iTRAQ or TMT mode</param>
/// <param name="iTraqCorrectionFactorType">Correction factor type for 4-plex iTRAQ</param>
public ITraqIntensityCorrection(ReporterIons.ReporterIonMassModeConstants reporterIonMode, CorrectionFactorsITRAQ4Plex iTraqCorrectionFactorType)
{
ReporterIonMode = reporterIonMode;
ITraq4PlexCorrectionFactorType = iTraqCorrectionFactorType;
mMatrixUtility = new MatrixDecompositionUtility.LUDecomposition();
if (ReporterIonMode == ReporterIons.ReporterIonMassModeConstants.CustomOrNone)
{
return;
}
InitializeCoefficients(false);
}
/// <summary>
/// Change the reporter ion mode
/// </summary>
/// <param name="reporterIonMode"></param>
// ReSharper disable once UnusedMember.Global
public void UpdateReporterIonMode(ReporterIons.ReporterIonMassModeConstants reporterIonMode)
{
UpdateReporterIonMode(reporterIonMode, ITraq4PlexCorrectionFactorType);
}
/// <summary>
/// Change the reporter ion mode
/// </summary>
/// <param name="reporterIonMode"></param>
/// <param name="iTraqCorrectionFactorType"></param>
public void UpdateReporterIonMode(ReporterIons.ReporterIonMassModeConstants reporterIonMode, CorrectionFactorsITRAQ4Plex iTraqCorrectionFactorType)
{
if (ReporterIonMode != reporterIonMode || ITraq4PlexCorrectionFactorType != iTraqCorrectionFactorType)
{
ReporterIonMode = reporterIonMode;
ITraq4PlexCorrectionFactorType = iTraqCorrectionFactorType;
InitializeCoefficients(true);
}
}
/// <summary>
/// Apply the correction factors to the reporter ions
/// </summary>
/// <param name="reporterIonIntensities"></param>
/// <param name="debugShowIntensities">When true, show the old and new reporter ion intensities at the console</param>
// ReSharper disable once UnusedMember.Global
public bool ApplyCorrection(float[] reporterIonIntensities, bool debugShowIntensities = false)
{
var dataCount = reporterIonIntensities.Length - 1;
var originalIntensities = new double[dataCount + 1];
for (var index = 0; index <= dataCount; index++)
{
originalIntensities[index] = reporterIonIntensities[index];
}
if (ApplyCorrection(originalIntensities, debugShowIntensities))
{
for (var index = 0; index <= dataCount; index++)
{
reporterIonIntensities[index] = (float)originalIntensities[index];
}
return true;
}
return false;
}
/// <summary>
/// Apply the correction factors to the reporter ions
/// </summary>
/// <param name="reporterIonIntensities"></param>
/// <param name="debugShowIntensities">When true, show the old and new reporter ion intensities at the console</param>
public bool ApplyCorrection(double[] reporterIonIntensities, bool debugShowIntensities = false)
{
var matrixSize = GetMatrixLength(ReporterIonMode);
var reporterIonMode = ReporterIons.GetReporterIonModeDescription(ReporterIonMode);
if (reporterIonIntensities.Length != matrixSize)
{
throw new InvalidOperationException(
"Length of ReporterIonIntensities array must be " + matrixSize +
" when using the " + reporterIonMode + " mode");
}
var correctedIntensities = mMatrixUtility.ProcessData(mCoeffs, matrixSize, reporterIonIntensities);
var maxIntensity = 0.0;
for (var index = 0; index < matrixSize; index++)
{
maxIntensity = Math.Max(maxIntensity, reporterIonIntensities[index]);
}
if (debugShowIntensities)
{
Console.WriteLine();
Console.WriteLine("{0,-8} {1,-10} {2,-12} {3}", "Index", "Intensity", "NewIntensity", "% Change");
}
// Now update reporterIonIntensities
for (var index = 0; index < matrixSize; index++)
{
if (!(reporterIonIntensities[index] > 0))
{
continue;
}
double newIntensity;
if (correctedIntensities[index] < 0)
{
newIntensity = 0;
}
else
{
newIntensity = correctedIntensities[index];
}
if (debugShowIntensities)
{
// Compute percent change vs. the maximum reporter ion intensity
var percentChange = (newIntensity - reporterIonIntensities[index]) / maxIntensity * 100;
var percentChangeRounded = (int)Math.Round(percentChange, 0);
string visualPercentChange;
if (percentChangeRounded > 0)
{
visualPercentChange = new string('+', percentChangeRounded);
}
else if (percentChangeRounded < 0)
{
visualPercentChange = new string('-', -percentChangeRounded);
}
else
{
visualPercentChange = string.Empty;
}
Console.WriteLine("{0,-8} {1,-10:0.0} {2,-12:0.0}{3,7:0.0}% {4}", index, reporterIonIntensities[index], newIntensity, percentChange, visualPercentChange);
}
reporterIonIntensities[index] = newIntensity;
}
return true;
}
private int GetMatrixLength(ReporterIons.ReporterIonMassModeConstants reporterIonMode)
{
// ReSharper disable once SwitchExpressionHandlesSomeKnownEnumValuesWithExceptionInDefault
return reporterIonMode switch
{
ReporterIons.ReporterIonMassModeConstants.ITraqFourMZ => FOUR_PLEX_MATRIX_LENGTH,
ReporterIons.ReporterIonMassModeConstants.ITraqEightMZHighRes => EIGHT_PLEX_HIGH_RES_MATRIX_LENGTH,
ReporterIons.ReporterIonMassModeConstants.ITraqEightMZLowRes => EIGHT_PLEX_LOW_RES_MATRIX_LENGTH,
ReporterIons.ReporterIonMassModeConstants.TMTTenMZ => TEN_PLEX_TMT_MATRIX_LENGTH,
ReporterIons.ReporterIonMassModeConstants.TMTElevenMZ => ELEVEN_PLEX_TMT_MATRIX_LENGTH,
ReporterIons.ReporterIonMassModeConstants.TMTSixteenMZ => SIXTEEN_PLEX_TMT_MATRIX_LENGTH,
ReporterIons.ReporterIonMassModeConstants.TMTEighteenMZ => EIGHTEEN_PLEX_TMT_MATRIX_LENGTH,
ReporterIons.ReporterIonMassModeConstants.TMT32MZ => THIRTY_TWO_PLEX_TMT_MATRIX_LENGTH,
ReporterIons.ReporterIonMassModeConstants.TMT35MZ => THIRTY_FIVE_PLEX_TMT_MATRIX_LENGTH,
_ => throw new ArgumentOutOfRangeException("Invalid value for reporterIonMode in GetMatrixLength: " + reporterIonMode)
};
}
/// <summary>
/// Initialize the coefficients
/// </summary>
/// <param name="debugShowMatrixTable">When true, show a table of the coefficients at the console</param>
private void InitializeCoefficients(bool debugShowMatrixTable)
{
// ReSharper disable TooWideLocalVariableScope
// iTraq reporter ions
IsotopeContributionType udtIsoPct113;
IsotopeContributionType udtIsoPct114;
IsotopeContributionType udtIsoPct115;
IsotopeContributionType udtIsoPct116;
IsotopeContributionType udtIsoPct117;
IsotopeContributionType udtIsoPct118;
IsotopeContributionType udtIsoPct119;
IsotopeContributionType udtIsoPct120;
IsotopeContributionType udtIsoPct121;
// TMT reporter ions
IsotopeContributionType udtIsoPct126;
IsotopeContributionType udtIsoPct127N;
IsotopeContributionType udtIsoPct127C;
IsotopeContributionType udtIsoPct128N;
IsotopeContributionType udtIsoPct128C;
IsotopeContributionType udtIsoPct129N;
IsotopeContributionType udtIsoPct129C;
IsotopeContributionType udtIsoPct130N;
IsotopeContributionType udtIsoPct130C;
IsotopeContributionType udtIsoPct131N;
IsotopeContributionType udtIsoPct131C;
// 16-plex and 18-plex TMT ions
IsotopeContributionType udtIsoPct132N;
IsotopeContributionType udtIsoPct132C;
IsotopeContributionType udtIsoPct133N;
IsotopeContributionType udtIsoPct133C;
IsotopeContributionType udtIsoPct134N;
IsotopeContributionType udtIsoPct134C;
IsotopeContributionType udtIsoPct135N;
// 32-plex and 35-plex TMT ions
// ToDo: determine the coefficients for these ions
#pragma warning disable CS0168 // Variable is declared but never used
IsotopeContributionType udtIsoPct127D;
IsotopeContributionType udtIsoPct128ND;
IsotopeContributionType udtIsoPct128CD;
IsotopeContributionType udtIsoPct129ND;
IsotopeContributionType udtIsoPct129CD;
IsotopeContributionType udtIsoPct130ND;
IsotopeContributionType udtIsoPct130CD;
IsotopeContributionType udtIsoPct131ND;
IsotopeContributionType udtIsoPct131CD;
IsotopeContributionType udtIsoPct132ND;
IsotopeContributionType udtIsoPct132CD;
IsotopeContributionType udtIsoPct133ND;
IsotopeContributionType udtIsoPct133CD;
IsotopeContributionType udtIsoPct134ND;
IsotopeContributionType udtIsoPct134CD;
IsotopeContributionType udtIsoPct135ND;
IsotopeContributionType udtIsoPct135CD;
#pragma warning restore CS0168 // Variable is declared but never used
// ReSharper restore TooWideLocalVariableScope
var matrixSize = GetMatrixLength(ReporterIonMode);
var maxIndex = matrixSize - 1;
switch (ReporterIonMode)
{
case ReporterIons.ReporterIonMassModeConstants.ITraqFourMZ:
if (ITraq4PlexCorrectionFactorType == CorrectionFactorsITRAQ4Plex.ABSciex)
{
// 4-plex ITraq, isotope contribution table
// Source percentages provided by Applied Biosystems
udtIsoPct114 = DefineIsotopeContribution(0, 1, 92.9F, 5.9F, 0.2F);
udtIsoPct115 = DefineIsotopeContribution(0, 2, 92.3F, 5.6F, 0.1F);
udtIsoPct116 = DefineIsotopeContribution(0, 3, 92.4F, 4.5F, 0.1F);
udtIsoPct117 = DefineIsotopeContribution(0.1F, 4, 92.3F, 3.5F, 0.1F);
}
else if (ITraq4PlexCorrectionFactorType == CorrectionFactorsITRAQ4Plex.BroadInstitute)
{
// 4-plex ITraq, isotope contribution table
// Source percentages provided by Philipp Mertins at the Broad Institute (pmertins@broadinstitute.org)
udtIsoPct114 = DefineIsotopeContribution(0, 0, 95.5F, 4.5F, 0);
udtIsoPct115 = DefineIsotopeContribution(0, 0.9F, 94.6F, 4.5F, 0);
udtIsoPct116 = DefineIsotopeContribution(0, 0.9F, 95.7F, 3.4F, 0);
udtIsoPct117 = DefineIsotopeContribution(0, 1.4F, 98.6F, 0, 0);
}
else
{
throw new ArgumentOutOfRangeException(nameof(ITraq4PlexCorrectionFactorType), "Unrecognized value for the iTRAQ 4 plex correction type");
}
// Goal is to generate either of these two matrices (depending on mITraq4PlexCorrectionFactorType):
// 0 1 2 3
// ----- ----- ----- -----
// 0 0.929 0.020 0 0
// 1 0.059 0.923 0.030 0.001
// 2 0.002 0.056 0.924 0.040
// 3 0 0.001 0.045 0.923
// 0 1 2 3
// ----- ----- ----- -----
// 0 0.955 0.009 0 0
// 1 0.045 0.946 0.009 0
// 2 0 0.045 0.957 0.014
// 3 0 0 0.034 0.986
mCoeffs = new double[maxIndex + 1, maxIndex + 1];
mCoeffs[0, 0] = udtIsoPct114.Zero;
mCoeffs[0, 1] = udtIsoPct115.Minus1;
mCoeffs[0, 2] = udtIsoPct116.Minus2;
mCoeffs[1, 0] = udtIsoPct114.Plus1;
mCoeffs[1, 1] = udtIsoPct115.Zero;
mCoeffs[1, 2] = udtIsoPct116.Minus1;
mCoeffs[1, 3] = udtIsoPct117.Minus2;
mCoeffs[2, 0] = udtIsoPct114.Plus2;
mCoeffs[2, 2] = udtIsoPct116.Zero;
mCoeffs[2, 1] = udtIsoPct115.Plus1;
mCoeffs[2, 3] = udtIsoPct117.Minus1;
mCoeffs[3, 1] = udtIsoPct115.Plus2;
mCoeffs[3, 2] = udtIsoPct116.Plus1;
mCoeffs[3, 3] = udtIsoPct117.Zero;
break;
case ReporterIons.ReporterIonMassModeConstants.ITraqEightMZHighRes:
// 8-plex ITraq, isotope contribution table for High Res MS/MS
// Source percentages provided by Applied Biosystems
// Note there is a 2 Da jump between 119 and 121, which is why 7.44 and 0.87 are not included in mCoeffs()
udtIsoPct113 = DefineIsotopeContribution(0, 0, 92.89F, 6.89F, 0.22F);
udtIsoPct114 = DefineIsotopeContribution(0, 0.94F, 93.01F, 5.9F, 0.16F);
udtIsoPct115 = DefineIsotopeContribution(0, 1.88F, 93.12F, 4.9F, 0.1F);
udtIsoPct116 = DefineIsotopeContribution(0, 2.82F, 93.21F, 3.9F, 0.07F);
udtIsoPct117 = DefineIsotopeContribution(0.06F, 3.77F, 93.29F, 2.88F, 0);
udtIsoPct118 = DefineIsotopeContribution(0.09F, 4.71F, 93.32F, 1.88F, 0);
udtIsoPct119 = DefineIsotopeContribution(0.14F, 5.66F, 93.34F, 0.87F, 0);
udtIsoPct121 = DefineIsotopeContribution(0.27F, 7.44F, 92.11F, 0.18F, 0);
// Goal is to generate this matrix:
// 0 1 2 3 4 5 6 7
// ------ ------ ------ ------ ------ ------ ------ ------
// 0 0.9289 0.0094 0 0 0 0 0 0
// 1 0.0689 0.9301 0.0188 0 0 0 0 0
// 2 0.0022 0.0590 0.9312 0.0282 0.0006 0 0 0
// 3 0 0.0016 0.0490 0.9321 0.0377 0.0009 0 0
// 4 0 0 0.0010 0.0390 0.9329 0.0471 0.0014 0
// 5 0 0 0 0.0007 0.0288 0.9332 0.0566 0
// 6 0 0 0 0 0 0.0188 0.9334 0.0027
// 7 0 0 0 0 0 0 0 0.9211
mCoeffs = new double[maxIndex + 1, maxIndex + 1];
mCoeffs[0, 0] = udtIsoPct113.Zero;
mCoeffs[0, 1] = udtIsoPct114.Minus1;
mCoeffs[0, 2] = udtIsoPct115.Minus2;
mCoeffs[1, 0] = udtIsoPct113.Plus1;
mCoeffs[1, 1] = udtIsoPct114.Zero;
mCoeffs[1, 2] = udtIsoPct115.Minus1;
mCoeffs[1, 3] = udtIsoPct116.Minus2;
mCoeffs[2, 0] = udtIsoPct113.Plus2;
mCoeffs[2, 1] = udtIsoPct114.Plus1;
mCoeffs[2, 2] = udtIsoPct115.Zero;
mCoeffs[2, 3] = udtIsoPct116.Minus1;
mCoeffs[2, 4] = udtIsoPct117.Minus2;
mCoeffs[3, 1] = udtIsoPct114.Plus2;
mCoeffs[3, 2] = udtIsoPct115.Plus1;
mCoeffs[3, 3] = udtIsoPct116.Zero;
mCoeffs[3, 4] = udtIsoPct117.Minus1;
mCoeffs[3, 5] = udtIsoPct118.Minus2;
mCoeffs[4, 2] = udtIsoPct115.Plus2;
mCoeffs[4, 3] = udtIsoPct116.Plus1;
mCoeffs[4, 4] = udtIsoPct117.Zero;
mCoeffs[4, 5] = udtIsoPct118.Minus1;
mCoeffs[4, 6] = udtIsoPct119.Minus2;
mCoeffs[5, 3] = udtIsoPct116.Plus2;
mCoeffs[5, 4] = udtIsoPct117.Plus1;
mCoeffs[5, 5] = udtIsoPct118.Zero;
mCoeffs[5, 6] = udtIsoPct119.Minus1;
mCoeffs[5, 7] = 0;
mCoeffs[6, 4] = udtIsoPct117.Plus2;
mCoeffs[6, 5] = udtIsoPct118.Plus1;
mCoeffs[6, 6] = udtIsoPct119.Zero;
mCoeffs[6, 7] = udtIsoPct121.Minus2;
mCoeffs[7, 5] = 0; // udtIsoPct118.Plus2
mCoeffs[7, 7] = udtIsoPct121.Zero;
break;
case ReporterIons.ReporterIonMassModeConstants.ITraqEightMZLowRes:
// 8-plex ITraq, isotope contribution table for Low Res MS/MS
// ReSharper disable CommentTypo
// Source percentages come from page 664 in:
// Vaudel, M., Sickmann, A., and L. Martens. "Peptide and protein quantification: A map of the minefield",
// Proteomics 2010, 10, 650-670.
// ReSharper restore CommentTypo
udtIsoPct113 = DefineIsotopeContribution(0, 0, 92.89F, 6.89F, 0.22F);
udtIsoPct114 = DefineIsotopeContribution(0, 0.94F, 93.01F, 5.9F, 0.16F);
udtIsoPct115 = DefineIsotopeContribution(0, 1.88F, 93.12F, 4.9F, 0.1F);
udtIsoPct116 = DefineIsotopeContribution(0, 2.82F, 93.21F, 3.9F, 0.07F);
udtIsoPct117 = DefineIsotopeContribution(0.06F, 3.77F, 93.29F, 2.88F, 0);
udtIsoPct118 = DefineIsotopeContribution(0.09F, 4.71F, 93.32F, 1.88F, 0);
udtIsoPct119 = DefineIsotopeContribution(0.14F, 5.66F, 93.34F, 0.87F, 0);
udtIsoPct120 = DefineIsotopeContribution(0, 0, 91.01F, 8.62F, 0);
udtIsoPct121 = DefineIsotopeContribution(0.27F, 7.44F, 92.11F, 0.18F, 0);
// Goal is to generate this expanded matrix, which takes Phenylalanine into account
// 0 1 2 3 4 5 6 7 8
// ------ ------ ------ ------ ------ ------ ------ ------ ------
// 0 0.9289 0.0094 0 0 0 0 0 0 0
// 1 0.0689 0.9301 0.0188 0 0 0 0 0 0
// 2 0.0022 0.0590 0.9312 0.0282 0.0006 0 0 0 0
// 3 0 0.0016 0.0490 0.9321 0.0377 0.0009 0 0 0
// 4 0 0 0.0010 0.0390 0.9329 0.0471 0.0014 0 0
// 5 0 0 0 0.0007 0.0288 0.9332 0.0566 0 0
// 6 0 0 0 0 0 0.0188 0.9334 0 0.0027
// 7 0 0 0 0 0 0 0.8700 0.9101 0.0744
// 8 0 0 0 0 0 0 0 0.0862 0.9211
mCoeffs = new double[maxIndex + 1, maxIndex + 1];
mCoeffs[0, 0] = udtIsoPct113.Zero;
mCoeffs[0, 1] = udtIsoPct114.Minus1;
mCoeffs[0, 2] = udtIsoPct115.Minus2;
mCoeffs[1, 0] = udtIsoPct113.Plus1;
mCoeffs[1, 1] = udtIsoPct114.Zero;
mCoeffs[1, 2] = udtIsoPct115.Minus1;
mCoeffs[1, 3] = udtIsoPct116.Minus2;
mCoeffs[2, 0] = udtIsoPct113.Plus2;
mCoeffs[2, 1] = udtIsoPct114.Plus1;
mCoeffs[2, 2] = udtIsoPct115.Zero;
mCoeffs[2, 3] = udtIsoPct116.Minus1;
mCoeffs[2, 4] = udtIsoPct117.Minus2;
mCoeffs[3, 1] = udtIsoPct114.Plus2;
mCoeffs[3, 2] = udtIsoPct115.Plus1;
mCoeffs[3, 3] = udtIsoPct116.Zero;
mCoeffs[3, 4] = udtIsoPct117.Minus1;
mCoeffs[3, 5] = udtIsoPct118.Minus2;
mCoeffs[4, 2] = udtIsoPct115.Plus2;
mCoeffs[4, 3] = udtIsoPct116.Plus1;
mCoeffs[4, 4] = udtIsoPct117.Zero;
mCoeffs[4, 5] = udtIsoPct118.Minus1;
mCoeffs[4, 6] = udtIsoPct119.Minus2;
mCoeffs[5, 3] = udtIsoPct116.Plus2;
mCoeffs[5, 4] = udtIsoPct117.Plus1;
mCoeffs[5, 5] = udtIsoPct118.Zero;
mCoeffs[5, 6] = udtIsoPct119.Minus1;
mCoeffs[5, 7] = 0;
mCoeffs[6, 4] = udtIsoPct117.Plus2;
mCoeffs[6, 5] = udtIsoPct118.Plus1;
mCoeffs[6, 6] = udtIsoPct119.Zero;
mCoeffs[6, 7] = 0;
mCoeffs[6, 8] = udtIsoPct121.Minus2;
mCoeffs[7, 5] = 0;
mCoeffs[7, 6] = udtIsoPct119.Plus1;
mCoeffs[7, 7] = udtIsoPct120.Zero;
mCoeffs[7, 8] = udtIsoPct121.Minus1;
mCoeffs[8, 6] = udtIsoPct119.Plus2;
mCoeffs[8, 7] = udtIsoPct120.Plus1;
mCoeffs[8, 8] = udtIsoPct121.Zero;
break;
case ReporterIons.ReporterIonMassModeConstants.TMTTenMZ:
case ReporterIons.ReporterIonMassModeConstants.TMTElevenMZ:
// 10-plex TMT and 11-plex TMT, isotope contribution table for High Res MS/MS
// Source percentages provided by Thermo
// TMT10plex lot RG234623
// TMT11plex lot SD250515
// udtIsoPct126 = DefineIsotopeContribution(0, 0, 95.1, 4.9, 0)
// udtIsoPct127N = DefineIsotopeContribution(0, 0.2, 94, 5.8, 0)
// udtIsoPct127C = DefineIsotopeContribution(0, 0.3, 94.9, 4.8, 0)
// udtIsoPct128N = DefineIsotopeContribution(0, 0.3, 96.1, 3.6, 0)
// udtIsoPct128C = DefineIsotopeContribution(0, 0.6, 95.5, 3.9, 0)
// udtIsoPct129N = DefineIsotopeContribution(0, 0.8, 96.2, 3, 0)
// udtIsoPct129C = DefineIsotopeContribution(0, 1.3, 95.8, 2.9, 0)
// udtIsoPct130N = DefineIsotopeContribution(0, 1.4, 93, 2.3, 3.3)
// udtIsoPct130C = DefineIsotopeContribution(0, 1.7, 96.1, 2.2, 0)
// udtIsoPct131N = DefineIsotopeContribution(0.2, 2, 95.6, 2.2, 0)
// udtIsoPct131C = DefineIsotopeContribution(0, 2.6, 94.5, 2.9, 0)
// TMT10plex lot A37725
// TMT11plex lot TB265130
// udtIsoPct126 = DefineIsotopeContribution(0, 0, 92.081, 7.551, 0.368)
// udtIsoPct127N = DefineIsotopeContribution(0, 0.093, 92.593, 7.315, 0)
// udtIsoPct127C = DefineIsotopeContribution(0, 0.468, 93.633, 5.899, 0)
// udtIsoPct128N = DefineIsotopeContribution(0, 0.658, 93.985, 5.357, 0)
// udtIsoPct128C = DefineIsotopeContribution(0.186, 1.484, 92.764, 5.566, 0)
// udtIsoPct129N = DefineIsotopeContribution(0, 2.326, 93.023, 4.651, 0)
// udtIsoPct129C = DefineIsotopeContribution(0, 2.158, 93.809, 4.034, 0)
// udtIsoPct130N = DefineIsotopeContribution(0, 2.533, 93.809, 3.659, 0)
// udtIsoPct130C = DefineIsotopeContribution(0, 1.628, 95.785, 2.586, 0)
// udtIsoPct131N = DefineIsotopeContribution(0, 3.625, 92.937, 3.439, 0)
// udtIsoPct131C = DefineIsotopeContribution(0, 3.471, 93.809, 2.72, 0)
// TMT10plex lot SG252258
// TMT11plex lot T4259309
udtIsoPct126 = DefineIsotopeContribution(0, 0, 100, 7.2F, 0.2F);
udtIsoPct127N = DefineIsotopeContribution(0, 0.4F, 100, 7.3F, 0.2F);
udtIsoPct127C = DefineIsotopeContribution(0, 0.5F, 100, 6.3F, 0);
udtIsoPct128N = DefineIsotopeContribution(0, 0.7F, 100, 5.7F, 0);
udtIsoPct128C = DefineIsotopeContribution(0, 1.4F, 100, 5.1F, 0);
udtIsoPct129N = DefineIsotopeContribution(0, 2.5F, 100, 5, 0);
udtIsoPct129C = DefineIsotopeContribution(0, 2.3F, 100, 4.3F, 0);
udtIsoPct130N = DefineIsotopeContribution(0, 2.7F, 100, 3.9F, 0);
udtIsoPct130C = DefineIsotopeContribution(0.4F, 2.9F, 100, 3.3F, 0);
udtIsoPct131N = DefineIsotopeContribution(0, 3.4F, 100, 3.3F, 0);
udtIsoPct131C = DefineIsotopeContribution(0, 3.7F, 100, 2.9F, 0);
// Goal is to generate this matrix (11-plex will not have the final row or final column)
// 0 1 2 3 4 5 6 7 8 9 10
// ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------
// 0 0.9260 0 0.0050 0 0 0 0 0 0 0 0
// 1 0 0.9210 0 0.0070 0 0 0 0 0 0 0
// 2 0.0720 0 0.9320 0 0.0140 0 0 0 0 0 0
// 3 0 0.0730 0 0.9360 0 0.0250 0 0 0 0 0
// 4 0.0020 0 0.0630 0 0.9350 0 0.0230 0 0.0040 0 0
// 5 0 0.0020 0 0.0570 0 0.9250 0 0.0270 0 0 0
// 6 0 0 0 0 0.0510 0 0.9340 0 0.0290 0 0
// 7 0 0 0 0 0 0.0500 0 0.9340 0 0.0340 0
// 8 0 0 0 0 0 0 0.0430 0 0.9340 0 0.0370
// 9 0 0 0 0 0 0 0 0.0390 0 0.9330 0
// 10 0 0 0 0 0 0 0 0 0.0330 0 0.9340
//
mCoeffs = new double[maxIndex + 1, maxIndex + 1];
mCoeffs[0, 0] = udtIsoPct126.Zero;
mCoeffs[0, 1] = 0;
mCoeffs[0, 2] = udtIsoPct127C.Minus1;
mCoeffs[0, 3] = 0;
mCoeffs[0, 4] = udtIsoPct128C.Minus2;
mCoeffs[1, 0] = 0;
mCoeffs[1, 1] = udtIsoPct127N.Zero;
mCoeffs[1, 2] = 0;
mCoeffs[1, 3] = udtIsoPct128N.Minus1;
mCoeffs[1, 4] = 0;
mCoeffs[1, 5] = udtIsoPct129N.Minus2;
mCoeffs[2, 0] = udtIsoPct126.Plus1;
mCoeffs[2, 1] = 0;
mCoeffs[2, 2] = udtIsoPct127C.Zero;
mCoeffs[2, 3] = 0;
mCoeffs[2, 4] = udtIsoPct128C.Minus1;
mCoeffs[2, 5] = 0;
mCoeffs[2, 6] = udtIsoPct129C.Minus2;
mCoeffs[3, 0] = 0;
mCoeffs[3, 1] = udtIsoPct127N.Plus1;
mCoeffs[3, 2] = 0;
mCoeffs[3, 3] = udtIsoPct128N.Zero;
mCoeffs[3, 4] = 0;
mCoeffs[3, 5] = udtIsoPct129N.Minus1;
mCoeffs[3, 6] = 0;
mCoeffs[3, 7] = udtIsoPct130N.Minus2;
mCoeffs[4, 0] = udtIsoPct126.Plus2;
mCoeffs[4, 1] = 0;
mCoeffs[4, 2] = udtIsoPct127C.Plus1;
mCoeffs[4, 3] = 0;
mCoeffs[4, 4] = udtIsoPct128C.Zero;
mCoeffs[4, 5] = 0;
mCoeffs[4, 6] = udtIsoPct129C.Minus1;
mCoeffs[4, 7] = 0;
mCoeffs[4, 8] = udtIsoPct130C.Minus2;
mCoeffs[5, 1] = udtIsoPct127N.Plus2;
mCoeffs[5, 2] = 0;
mCoeffs[5, 3] = udtIsoPct128N.Plus1;
mCoeffs[5, 4] = 0;
mCoeffs[5, 5] = udtIsoPct129N.Zero;
mCoeffs[5, 6] = 0;
mCoeffs[5, 7] = udtIsoPct130N.Minus1;
mCoeffs[5, 8] = 0;
mCoeffs[5, 9] = udtIsoPct131N.Minus2;
mCoeffs[6, 2] = udtIsoPct127C.Plus2;
mCoeffs[6, 3] = 0;
mCoeffs[6, 4] = udtIsoPct128C.Plus1;
mCoeffs[6, 5] = 0;
mCoeffs[6, 6] = udtIsoPct129C.Zero;
mCoeffs[6, 7] = 0;
mCoeffs[6, 8] = udtIsoPct130C.Minus1;
mCoeffs[7, 3] = udtIsoPct128N.Plus2;
mCoeffs[7, 4] = 0;
mCoeffs[7, 5] = udtIsoPct129N.Plus1;
mCoeffs[7, 6] = 0;
mCoeffs[7, 7] = udtIsoPct130N.Zero;
mCoeffs[7, 8] = 0;
mCoeffs[7, 9] = udtIsoPct131N.Minus1;
mCoeffs[8, 4] = udtIsoPct128C.Plus2;
mCoeffs[8, 5] = 0;
mCoeffs[8, 6] = udtIsoPct129C.Plus1;
mCoeffs[8, 7] = 0;
mCoeffs[8, 8] = udtIsoPct130C.Zero;
mCoeffs[8, 9] = 0;
if (maxIndex >= 10)
{
mCoeffs[8, 10] = udtIsoPct131C.Minus1;
}
mCoeffs[9, 5] = udtIsoPct129N.Plus2;
mCoeffs[9, 6] = 0;
mCoeffs[9, 7] = udtIsoPct130N.Plus1;
mCoeffs[9, 8] = 0;
mCoeffs[9, 9] = udtIsoPct131N.Zero;
if (maxIndex >= 10)
{
mCoeffs[10, 6] = udtIsoPct129C.Plus2;
mCoeffs[10, 7] = 0;
mCoeffs[10, 8] = udtIsoPct130C.Plus1;
mCoeffs[10, 9] = 0;
mCoeffs[10, 10] = udtIsoPct131C.Zero;
}
break;
case ReporterIons.ReporterIonMassModeConstants.TMTSixteenMZ:
// 16-plex TMT, isotope contribution table for High Res MS/MS
// Source percentages provided by Thermo
// ReSharper disable once CommentTypo
// TMTpro lot UH290428
// Column map
// PDF file column Contribution field
// --------------- ------------------
// -2x 13C minus2
// -13C minus1
// M+ zero
// +13C plus1
// +2x 13C plus2
udtIsoPct126 = DefineIsotopeContribution(0, 0, 100, 7.73F, 0.22F);
udtIsoPct127N = DefineIsotopeContribution(0, 0, 100, 7.46F, 0.22F);
udtIsoPct127C = DefineIsotopeContribution(0, 0.71F, 100, 6.62F, 0.16F);
udtIsoPct128N = DefineIsotopeContribution(0, 0.75F, 100, 6.67F, 0.16F);
udtIsoPct128C = DefineIsotopeContribution(0.06F, 1.34F, 100, 5.31F, 0.11F);
udtIsoPct129N = DefineIsotopeContribution(0.01F, 1.29F, 100, 5.48F, 0.1F);
udtIsoPct129C = DefineIsotopeContribution(0.26F, 2.34F, 100, 4.87F, 0.08F);
udtIsoPct130N = DefineIsotopeContribution(0.39F, 2.36F, 100, 4.57F, 0.07F);
udtIsoPct130C = DefineIsotopeContribution(0.05F, 2.67F, 100, 3.85F, 0.15F);
udtIsoPct131N = DefineIsotopeContribution(0.05F, 2.71F, 100, 3.73F, 0.04F);
udtIsoPct131C = DefineIsotopeContribution(0.09F, 3.69F, 100, 2.77F, 0.01F);
udtIsoPct132N = DefineIsotopeContribution(0.09F, 2.51F, 100, 2.76F, 0.01F);
udtIsoPct132C = DefineIsotopeContribution(0.1F, 4.11F, 100, 1.63F, 0);
udtIsoPct133N = DefineIsotopeContribution(0.09F, 3.09F, 100, 1.58F, 0);
udtIsoPct133C = DefineIsotopeContribution(0.36F, 4.63F, 100, 0.88F, 0);
udtIsoPct134N = DefineIsotopeContribution(0.38F, 4.82F, 100, 0.86F, 0);
// Goal is to generate a 16x16 matrix
// 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
// -- ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------
// 0 0.9205 0 0.0071 0 0.0006 0 0 0 0 0 0 0 0 0 0 0
// 1 0 0.9232 0 0.0075 0 0.0001 0 0 0 0 0 0 0 0 0 0
// 2 0.0773 0 0.9251 0 0.0134 0 0.0026 0 0 0 0 0 0 0 0 0
// 3 0 0.0746 0 0.9242 0 0.0129 0 0.0039 0 0 0 0 0 0 0 0
// 4 0.0022 0 0.0662 0 0.9318 0 0.0234 0 0.0005 0 0 0 0 0 0 0
// 5 0 0.0022 0 0.0667 0 0.9312 0 0.0236 0 0.0005 0 0 0 0 0 0
// 6 0 0 0.0016 0 0.0531 0 0.9245 0 0.0267 0 0.0009 0 0 0 0 0
// 7 0 0 0 0.0016 0 0.0548 0 0.9261 0 0.0271 0 0.0009 0 0 0 0
// 8 0 0 0 0 0.0011 0 0.0487 0 0.9328 0 0.0369 0 0.0010 0 0 0
// 9 0 0 0 0 0 0.0010 0 0.0457 0 0.9347 0 0.0251 0 0.0009 0 0
// 10 0 0 0 0 0 0 0.0008 0 0.0385 0 0.9344 0 0.0411 0 0.0036 0
// 11 0 0 0 0 0 0 0 0.0007 0 0.0373 0 0.9463 0 0.0309 0 0.0038
// 12 0 0 0 0 0 0 0 0 0.0015 0 0.0277 0 0.9416 0 0.0463 0
// 13 0 0 0 0 0 0 0 0 0 0.0004 0 0.0276 0 0.9524 0 0.0482
// 14 0 0 0 0 0 0 0 0 0 0 0.0001 0 0.0163 0 0.9413 0
// 15 0 0 0 0 0 0 0 0 0 0 0 0.0001 0 0.0158 0 0.9394
mCoeffs = new double[maxIndex + 1, maxIndex + 1];
mCoeffs[0, 0] = udtIsoPct126.Zero;
mCoeffs[0, 1] = 0;
mCoeffs[0, 2] = udtIsoPct127C.Minus1;
mCoeffs[0, 3] = 0;
mCoeffs[0, 4] = udtIsoPct128C.Minus2;
mCoeffs[1, 0] = 0;
mCoeffs[1, 1] = udtIsoPct127N.Zero;
mCoeffs[1, 2] = 0;
mCoeffs[1, 3] = udtIsoPct128N.Minus1;
mCoeffs[1, 4] = 0;
mCoeffs[1, 5] = udtIsoPct129N.Minus2;
mCoeffs[2, 0] = udtIsoPct126.Plus1;
mCoeffs[2, 1] = 0;
mCoeffs[2, 2] = udtIsoPct127C.Zero;
mCoeffs[2, 3] = 0;
mCoeffs[2, 4] = udtIsoPct128C.Minus1;
mCoeffs[2, 5] = 0;
mCoeffs[2, 6] = udtIsoPct129C.Minus2;
mCoeffs[3, 0] = 0;
mCoeffs[3, 1] = udtIsoPct127N.Plus1;
mCoeffs[3, 2] = 0;
mCoeffs[3, 3] = udtIsoPct128N.Zero;
mCoeffs[3, 4] = 0;
mCoeffs[3, 5] = udtIsoPct129N.Minus1;
mCoeffs[3, 6] = 0;
mCoeffs[3, 7] = udtIsoPct130N.Minus2;
mCoeffs[4, 0] = udtIsoPct126.Plus2;
mCoeffs[4, 1] = 0;
mCoeffs[4, 2] = udtIsoPct127C.Plus1;
mCoeffs[4, 3] = 0;
mCoeffs[4, 4] = udtIsoPct128C.Zero;
mCoeffs[4, 5] = 0;
mCoeffs[4, 6] = udtIsoPct129C.Minus1;
mCoeffs[4, 7] = 0;
mCoeffs[4, 8] = udtIsoPct130C.Minus2;
mCoeffs[5, 1] = udtIsoPct127N.Plus2;
mCoeffs[5, 2] = 0;
mCoeffs[5, 3] = udtIsoPct128N.Plus1;
mCoeffs[5, 4] = 0;
mCoeffs[5, 5] = udtIsoPct129N.Zero;
mCoeffs[5, 6] = 0;
mCoeffs[5, 7] = udtIsoPct130N.Minus1;
mCoeffs[5, 8] = 0;
mCoeffs[5, 9] = udtIsoPct131N.Minus2;
mCoeffs[6, 2] = udtIsoPct127C.Plus2;
mCoeffs[6, 3] = 0;
mCoeffs[6, 4] = udtIsoPct128C.Plus1;
mCoeffs[6, 5] = 0;
mCoeffs[6, 6] = udtIsoPct129C.Zero;
mCoeffs[6, 7] = 0;
mCoeffs[6, 8] = udtIsoPct130C.Minus1;
mCoeffs[6, 9] = 0;
mCoeffs[6, 10] = udtIsoPct131C.Minus2;
mCoeffs[7, 3] = udtIsoPct128N.Plus2;
mCoeffs[7, 4] = 0;
mCoeffs[7, 5] = udtIsoPct129N.Plus1;
mCoeffs[7, 6] = 0;
mCoeffs[7, 7] = udtIsoPct130N.Zero;
mCoeffs[7, 8] = 0;
mCoeffs[7, 9] = udtIsoPct131N.Minus1;
mCoeffs[7, 10] = 0;
mCoeffs[7, 11] = udtIsoPct132N.Minus2;
mCoeffs[8, 4] = udtIsoPct128C.Plus2;
mCoeffs[8, 5] = 0;
mCoeffs[8, 6] = udtIsoPct129C.Plus1;
mCoeffs[8, 7] = 0;
mCoeffs[8, 8] = udtIsoPct130C.Zero;
mCoeffs[8, 9] = 0;
mCoeffs[8, 10] = udtIsoPct131C.Minus1;
mCoeffs[8, 11] = 0;
mCoeffs[8, 12] = udtIsoPct132C.Minus2;
mCoeffs[9, 5] = udtIsoPct129N.Plus2;
mCoeffs[9, 6] = 0;
mCoeffs[9, 7] = udtIsoPct130N.Plus1;
mCoeffs[9, 8] = 0;
mCoeffs[9, 9] = udtIsoPct131N.Zero;
mCoeffs[9, 10] = 0;
mCoeffs[9, 11] = udtIsoPct132N.Minus1;
mCoeffs[9, 12] = 0;
mCoeffs[9, 13] = udtIsoPct133N.Minus2;
mCoeffs[10, 6] = udtIsoPct129C.Plus2;
mCoeffs[10, 7] = 0;
mCoeffs[10, 8] = udtIsoPct130C.Plus1;
mCoeffs[10, 9] = 0;
mCoeffs[10, 10] = udtIsoPct131C.Zero;
mCoeffs[10, 11] = 0;
mCoeffs[10, 12] = udtIsoPct132C.Minus1;
mCoeffs[10, 13] = 0;
mCoeffs[10, 14] = udtIsoPct133C.Minus2;
mCoeffs[11, 7] = udtIsoPct130N.Plus2;
mCoeffs[11, 8] = 0;
mCoeffs[11, 9] = udtIsoPct131N.Plus1;
mCoeffs[11, 10] = 0;
mCoeffs[11, 11] = udtIsoPct132N.Zero;
mCoeffs[11, 12] = 0;
mCoeffs[11, 13] = udtIsoPct133N.Minus1;
mCoeffs[11, 14] = 0;
mCoeffs[11, 15] = udtIsoPct134N.Minus2;
mCoeffs[12, 8] = udtIsoPct130C.Plus2;
mCoeffs[12, 9] = 0;
mCoeffs[12, 10] = udtIsoPct131C.Plus1;
mCoeffs[12, 11] = 0;
mCoeffs[12, 12] = udtIsoPct132C.Zero;
mCoeffs[12, 13] = 0;
mCoeffs[12, 14] = udtIsoPct133C.Minus1;
mCoeffs[13, 9] = udtIsoPct131N.Plus2;
mCoeffs[13, 10] = 0;
mCoeffs[13, 11] = udtIsoPct132N.Plus1;
mCoeffs[13, 12] = 0;
mCoeffs[13, 13] = udtIsoPct133N.Zero;
mCoeffs[13, 14] = 0;
mCoeffs[13, 15] = udtIsoPct134N.Minus1;
mCoeffs[14, 10] = udtIsoPct131C.Plus2;
mCoeffs[14, 11] = 0;
mCoeffs[14, 12] = udtIsoPct132C.Plus1;
mCoeffs[14, 13] = 0;
mCoeffs[14, 14] = udtIsoPct133C.Zero;
mCoeffs[15, 11] = udtIsoPct132N.Plus2;
mCoeffs[15, 12] = 0;
mCoeffs[15, 13] = udtIsoPct133N.Plus1;
mCoeffs[15, 14] = 0;
mCoeffs[15, 15] = udtIsoPct134N.Zero;
break;
case ReporterIons.ReporterIonMassModeConstants.TMTEighteenMZ:
case ReporterIons.ReporterIonMassModeConstants.TMT32MZ:
case ReporterIons.ReporterIonMassModeConstants.TMT35MZ:
// 18-plex TMT, isotope contribution table for High Res MS/MS
// Source percentages provided by Thermo
// ReSharper disable once CommentTypo
// TMTpro lot UH290428
// Column map
// PDF file column Contribution field
// --------------- ------------------
// -2x 13C minus2
// -13C minus1
// M+ zero
// +13C plus1
// +2x 13C plus2
udtIsoPct126 = DefineIsotopeContribution(0, 0, 100, 7.73F, 0.22F);
udtIsoPct127N = DefineIsotopeContribution(0, 0, 100, 7.46F, 0.22F);
udtIsoPct127C = DefineIsotopeContribution(0, 0.71F, 100, 6.62F, 0.16F);
udtIsoPct128N = DefineIsotopeContribution(0, 0.75F, 100, 6.67F, 0.16F);
udtIsoPct128C = DefineIsotopeContribution(0.06F, 1.34F, 100, 5.31F, 0.11F);
udtIsoPct129N = DefineIsotopeContribution(0.01F, 1.29F, 100, 5.48F, 0.1F);
udtIsoPct129C = DefineIsotopeContribution(0.26F, 2.34F, 100, 4.87F, 0.08F);
udtIsoPct130N = DefineIsotopeContribution(0.39F, 2.36F, 100, 4.57F, 0.07F);
udtIsoPct130C = DefineIsotopeContribution(0.05F, 2.67F, 100, 3.85F, 0.15F);
udtIsoPct131N = DefineIsotopeContribution(0.05F, 2.71F, 100, 3.73F, 0.04F);
udtIsoPct131C = DefineIsotopeContribution(0.09F, 3.69F, 100, 2.77F, 0.01F);
udtIsoPct132N = DefineIsotopeContribution(0.09F, 2.51F, 100, 2.76F, 0.01F);
udtIsoPct132C = DefineIsotopeContribution(0.1F, 4.11F, 100, 1.63F, 0);
udtIsoPct133N = DefineIsotopeContribution(0.09F, 3.09F, 100, 1.58F, 0);
udtIsoPct133C = DefineIsotopeContribution(0.36F, 4.63F, 100, 0.88F, 0);
udtIsoPct134N = DefineIsotopeContribution(0.38F, 4.82F, 100, 0.86F, 0);
udtIsoPct134C = DefineIsotopeContribution(0.14F, 5.81F, 100, 0, 0);
udtIsoPct135N = DefineIsotopeContribution(0.19F, 5.42F, 100, 0, 0);
// Goal is to generate an 18x18 matrix
// 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
// -- ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------
// 0 0.9205 0 0.0071 0 0.0006 0 0 0 0 0 0 0 0 0 0 0 0 0
// 1 0 0.9232 0 0.0075 0 0.0001 0 0 0 0 0 0 0 0 0 0 0 0
// 2 0.0773 0 0.9251 0 0.0134 0 0.0026 0 0 0 0 0 0 0 0 0 0 0
// 3 0 0.0746 0 0.9242 0 0.0129 0 0.0039 0 0 0 0 0 0 0 0 0 0
// 4 0.0022 0 0.0662 0 0.9318 0 0.0234 0 0.0005 0 0 0 0 0 0 0 0 0
// 5 0 0.0022 0 0.0667 0 0.9312 0 0.0236 0 0.0005 0 0 0 0 0 0 0 0
// 6 0 0 0.0016 0 0.0531 0 0.9245 0 0.0267 0 0.0009 0 0 0 0 0 0 0
// 7 0 0 0 0.0016 0 0.0548 0 0.9261 0 0.0271 0 0.0009 0 0 0 0 0 0
// 8 0 0 0 0 0.0011 0 0.0487 0 0.9328 0 0.0369 0 0.0010 0 0 0 0 0
// 9 0 0 0 0 0 0.0010 0 0.0457 0 0.9347 0 0.0251 0 0.0009 0 0 0 0
// 10 0 0 0 0 0 0 0.0008 0 0.0385 0 0.9344 0 0.0411 0 0.0036 0 0 0
// 11 0 0 0 0 0 0 0 0.0007 0 0.0373 0 0.9463 0 0.0309 0 0.0038 0 0
// 12 0 0 0 0 0 0 0 0 0.0015 0 0.0277 0 0.9416 0 0.0463 0 0.0014 0
// 13 0 0 0 0 0 0 0 0 0 0.0004 0 0.0276 0 0.9524 0 0.0482 0 0.0019
// 14 0 0 0 0 0 0 0 0 0 0 0.0001 0 0.0163 0 0.9413 0 0.0581 0
// 15 0 0 0 0 0 0 0 0 0 0 0 0.0001 0 0.0158 0 0.9394 0 0.0542
// 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.0088 0 0.9405 0
// 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.0086 0 0.9439
mCoeffs = new double[maxIndex + 1, maxIndex + 1];
mCoeffs[0, 0] = udtIsoPct126.Zero;
mCoeffs[0, 1] = 0;
mCoeffs[0, 2] = udtIsoPct127C.Minus1;
mCoeffs[0, 3] = 0;
mCoeffs[0, 4] = udtIsoPct128C.Minus2;
mCoeffs[1, 0] = 0;
mCoeffs[1, 1] = udtIsoPct127N.Zero;
mCoeffs[1, 2] = 0;
mCoeffs[1, 3] = udtIsoPct128N.Minus1;
mCoeffs[1, 4] = 0;
mCoeffs[1, 5] = udtIsoPct129N.Minus2;
mCoeffs[2, 0] = udtIsoPct126.Plus1;