-
Notifications
You must be signed in to change notification settings - Fork 4
/
ReporterIonProcessor.cs
839 lines (691 loc) · 36.5 KB
/
ReporterIonProcessor.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
using System;
using System.Collections.Generic;
using System.IO;
using MASIC.Data;
using MASIC.Options;
using MathNet.Numerics.Statistics;
using PRISM;
using ThermoRawFileReader;
namespace MASIC
{
/// <summary>
/// Class for finding reporter ions
/// </summary>
public class ReporterIonProcessor : MasicEventNotifier
{
// Ignore Spelling: plex, Uniquify
/// <summary>
/// Column prefix for reporter ion data in the output file
/// </summary>
public const string REPORTER_ION_COLUMN_PREFIX = "Ion_";
private readonly MASICOptions mOptions;
/// <summary>
/// Constructor
/// </summary>
/// <param name="masicOptions"></param>
public ReporterIonProcessor(MASICOptions masicOptions)
{
mOptions = masicOptions;
}
/// <summary>
/// Look for MS3 spectra
/// If found, possibly copy the reporter ion data to parent MS2 spectra
/// </summary>
/// <remarks>
/// If mOptions.ReporterIons.AlwaysUseMS3ReporterIonsForParents is true, always copy
/// If false (the default), examine reporter ions in the parent MS2 spectra and copy if the median intensity is less than the MS3 scan's median intensity
/// </remarks>
/// <param name="cachedDataToWrite"></param>
private void CopyReporterIonsToParentIfRequired(SortedDictionary<int, ReporterIonStats> cachedDataToWrite)
{
foreach (var item in cachedDataToWrite)
{
if (item.Value.MSLevel <= 2 || item.Value.ParentScan == 0)
continue;
var targetScan = 0;
if (mOptions.ReporterIons.AlwaysUseMS3ReporterIonsForParents)
{
targetScan = item.Value.ParentScan;
}
else
{
// Compute the median reporter ion intensity for this MS3 scan (both using all values and ignoring missing values and zeros)
var reporterIonCount = item.Value.ReporterIonIntensityEndIndex - item.Value.ReporterIonIntensityStartIndex + 1;
var medianMS3Intensity = GetMedianReporterIonIntensity(
string.Format("MS3 scan {0}", item.Key),
item.Value.DataColumns.GetRange(item.Value.ReporterIonIntensityStartIndex, reporterIonCount),
out var medianMS3IntensityIgnoringZeros);
// Examine the parent ion intensities of the parent MS2 scan
// If the median value is less than medianMS3Intensity,
// copy the reporter ion intensities from the MS3 scan to the MS2 scan
// ReSharper disable once ForeachCanBePartlyConvertedToQueryUsingAnotherGetEnumerator
foreach (var candidateScan in cachedDataToWrite)
{
if (candidateScan.Key != item.Value.ParentScan)
continue;
var medianMS2Intensity = GetMedianReporterIonIntensity(
string.Format("MS2 scan {0}", candidateScan.Value.ScanNumber),
candidateScan.Value.DataColumns.GetRange(item.Value.ReporterIonIntensityStartIndex, reporterIonCount),
out var medianMS2IntensityIgnoringZeros);
// First compare the median based on all values, since scans with numerous reporter ion intensities that are small (or 0) will have a smaller median
if (medianMS2Intensity < medianMS3Intensity)
{
targetScan = item.Value.ParentScan;
}
else if (medianMS2IntensityIgnoringZeros < medianMS3IntensityIgnoringZeros)
{
// If both the MS2 scan and the MS3 scan have several reporter ions with an intensity of 0, the median for each will be 0
// Compare the median of the non-zero values
targetScan = item.Value.ParentScan;
}
break;
}
}
if (targetScan == 0)
{
continue;
}
foreach (var candidateScan in cachedDataToWrite)
{
if (candidateScan.Key != targetScan)
continue;
var targetScanStats = candidateScan.Value;
// Copy the ReporterIonIntensityMax value
targetScanStats.DataColumns[item.Value.ReporterIonIntensityStartIndex - 1] =
item.Value.DataColumns[item.Value.ReporterIonIntensityStartIndex - 1];
// Copy the reporter ion data (starting at column index ReporterIonIntensityStartIndex)
for (var i = item.Value.ReporterIonIntensityStartIndex; i < item.Value.DataColumns.Count; i++)
{
targetScanStats.DataColumns[i] = item.Value.DataColumns[i];
}
}
}
}
/// <summary>
/// Looks for the reporter ion peaks using FindReporterIonsWork
/// </summary>
/// <param name="scanList"></param>
/// <param name="spectraCache"></param>
/// <param name="inputFilePathFull">Full path to the input file</param>
/// <param name="outputDirectoryPath"></param>
public bool FindReporterIons(
ScanList scanList,
SpectraCache spectraCache,
string inputFilePathFull,
string outputDirectoryPath)
{
const char TAB_DELIMITER = '\t';
var outputFilePath = "??";
try
{
// Use XRawFileIO to read the .Raw files
var readerOptions = new ThermoReaderOptions
{
LoadMSMethodInfo = false,
LoadMSTuneInfo = false
};
var rawFileReader = new XRawFileIO(readerOptions);
RegisterEvents(rawFileReader);
var includeFtmsColumns = false;
if (inputFilePathFull.EndsWith(DataInput.DataImport.THERMO_RAW_FILE_EXTENSION, StringComparison.OrdinalIgnoreCase))
{
// Processing a Thermo .Raw file
// Check whether any of the fragmentation scans has IsHighResolution true
for (var masterOrderIndex = 0; masterOrderIndex < scanList.MasterScanOrderCount; masterOrderIndex++)
{
var scanPointer = scanList.MasterScanOrder[masterOrderIndex].ScanIndexPointer;
if (scanList.MasterScanOrder[masterOrderIndex].ScanType == ScanList.ScanTypeConstants.SurveyScan)
{
// Skip survey scans
continue;
}
if (scanList.FragScans[scanPointer].IsHighResolution)
{
includeFtmsColumns = true;
break;
}
}
if (includeFtmsColumns)
{
rawFileReader.OpenRawFile(inputFilePathFull);
}
}
if (mOptions.ReporterIons.ReporterIonList.Count == 0)
{
// No reporter ions defined; default to 11-plex TMT
mOptions.ReporterIons.SetReporterIonMassMode(ReporterIons.ReporterIonMassModeConstants.TMTElevenMZ);
}
// Populate array reporterIons, which we will sort by m/z
var reporterIons = new ReporterIonInfo[mOptions.ReporterIons.ReporterIonList.Count];
var index = 0;
foreach (var reporterIon in mOptions.ReporterIons.ReporterIonList)
{
reporterIons[index] = reporterIon;
index++;
}
Array.Sort(reporterIons, new ReportIonInfoComparer());
outputFilePath = DataOutput.DataOutput.ConstructOutputFilePath(
Path.GetFileName(inputFilePathFull),
outputDirectoryPath,
DataOutput.DataOutput.OutputFileTypeConstants.ReporterIonsFile);
using var writer = new StreamWriter(outputFilePath);
// Write the file headers
var reporterIonMZsUnique = new SortedSet<string>();
var headerColumns = new List<string>(7 + reporterIons.Length + 1)
{
"Dataset",
"ScanNumber",
"Collision Mode",
"ParentIonMZ",
"BasePeakIntensity",
"BasePeakMZ",
"ParentScan",
"ReporterIonIntensityMax"
};
var obsMZHeaders = new List<string>(reporterIons.Length);
var uncorrectedIntensityHeaders = new List<string>(reporterIons.Length);
var ftmsSignalToNoise = new List<string>(reporterIons.Length);
var ftmsResolution = new List<string>(reporterIons.Length);
//var ftmsLabelDataMz = new List<string>(reporterIons.Length);
var saveUncorrectedIntensities =
mOptions.ReporterIons.ReporterIonApplyAbundanceCorrection && mOptions.ReporterIons.ReporterIonSaveUncorrectedIntensities;
var dataAggregation = new DataAggregation();
RegisterEvents(dataAggregation);
for (var reporterIonIndex = 0; reporterIonIndex < reporterIons.Length; reporterIonIndex++)
{
var reporterIon = reporterIons[reporterIonIndex];
if (reporterIon.ContaminantIon && !saveUncorrectedIntensities)
continue;
// Construct the reporter ion intensity header
// We skip contaminant ions, unless saveUncorrectedIntensities is True, in which case we include them
string mzValue;
if (mOptions.ReporterIons.ReporterIonMassMode is
ReporterIons.ReporterIonMassModeConstants.TMTTenMZ or
ReporterIons.ReporterIonMassModeConstants.TMTElevenMZ or
ReporterIons.ReporterIonMassModeConstants.TMTSixteenMZ or
ReporterIons.ReporterIonMassModeConstants.TMTEighteenMZ)
{
mzValue = reporterIon.MZ.ToString("#0.000");
}
else
{
mzValue = ((int)Math.Round(reporterIon.MZ, 0)).ToString();
}
if (reporterIonMZsUnique.Contains(mzValue))
{
// Uniquify the m/z value
mzValue += "_" + reporterIonIndex;
}
try
{
reporterIonMZsUnique.Add(mzValue);
}
catch (Exception)
{
// Error updating the SortedSet;
// this shouldn't happen based on the .ContainsKey test above
}
// Append the reporter ion intensity title to the headers
headerColumns.Add(REPORTER_ION_COLUMN_PREFIX + mzValue);
// This string will only be included in the header line if mOptions.ReporterIons.ReporterIonSaveObservedMasses is true
obsMZHeaders.Add(REPORTER_ION_COLUMN_PREFIX + mzValue + "_ObsMZ");
// This string will be included in the header line if saveUncorrectedIntensities is true
uncorrectedIntensityHeaders.Add(REPORTER_ION_COLUMN_PREFIX + mzValue + "_OriginalIntensity");
// This string will be included in the header line if includeFtmsColumns is true
ftmsSignalToNoise.Add(REPORTER_ION_COLUMN_PREFIX + mzValue + "_SignalToNoise");
ftmsResolution.Add(REPORTER_ION_COLUMN_PREFIX + mzValue + "_Resolution");
// Uncomment to include the label data m/z value in the _ReporterIons.txt file
// This string will only be included in the header line if mOptions.ReporterIons.ReporterIonSaveObservedMasses is true
//ftmsLabelDataMz.Add(REPORTER_ION_COLUMN_PREFIX + mzValue + "_LabelDataMZ");
}
headerColumns.Add("Weighted Avg Pct Intensity Correction");
if (mOptions.ReporterIons.ReporterIonSaveObservedMasses)
{
headerColumns.AddRange(obsMZHeaders);
}
if (saveUncorrectedIntensities)
{
headerColumns.AddRange(uncorrectedIntensityHeaders);
}
if (includeFtmsColumns)
{
headerColumns.AddRange(ftmsSignalToNoise);
headerColumns.AddRange(ftmsResolution);
// Uncomment to include the label data m/z value in the _ReporterIons.txt file
// if (mOptions.ReporterIons.ReporterIonSaveObservedMasses)
// {
// headerColumns.AddRange(ftmsLabelDataMz);
// }
}
// Write the headers to the output file, separated by tabs
writer.WriteLine(string.Join(TAB_DELIMITER.ToString(), headerColumns));
UpdateProgress(0, "Searching for reporter ions");
// Keys in this dictionary are scan number, values are the data columns for each scan
var cachedDataToWrite = new SortedDictionary<int, ReporterIonStats>();
for (var masterOrderIndex = 0; masterOrderIndex < scanList.MasterScanOrderCount; masterOrderIndex++)
{
var scanPointer = scanList.MasterScanOrder[masterOrderIndex].ScanIndexPointer;
if (scanList.MasterScanOrder[masterOrderIndex].ScanType == ScanList.ScanTypeConstants.SurveyScan)
{
// Survey scan; write the cached data, then move on to the next scan
if (cachedDataToWrite.Count > 0)
{
WriteCachedReporterIons(writer, cachedDataToWrite, TAB_DELIMITER);
cachedDataToWrite.Clear();
}
continue;
}
FindReporterIonsWork(
rawFileReader,
dataAggregation,
includeFtmsColumns,
mOptions.SICOptions,
scanList,
spectraCache,
scanList.FragScans[scanPointer],
cachedDataToWrite,
reporterIons,
saveUncorrectedIntensities,
mOptions.ReporterIons.ReporterIonSaveObservedMasses);
if (scanList.MasterScanOrderCount > 1)
{
UpdateProgress((short)(masterOrderIndex / (double)(scanList.MasterScanOrderCount - 1) * 100));
}
else
{
UpdateProgress(0);
}
UpdateCacheStats(spectraCache);
if (mOptions.AbortProcessing)
{
break;
}
}
if (cachedDataToWrite.Count > 0)
{
WriteCachedReporterIons(writer, cachedDataToWrite, TAB_DELIMITER);
cachedDataToWrite.Clear();
}
if (includeFtmsColumns)
{
// Close the handle to the data file
rawFileReader.CloseRawFile();
}
return true;
}
catch (Exception ex)
{
ReportError("Error writing the reporter ions to: " + outputFilePath, ex, clsMASIC.MasicErrorCodes.OutputFileWriteError);
return false;
}
}
private void WriteCachedReporterIons(
TextWriter writer,
SortedDictionary<int, ReporterIonStats> cachedDataToWrite,
char delimiter)
{
if (mOptions.ReporterIons.UseMS3ReporterIonsForParentMS2Spectra)
{
CopyReporterIonsToParentIfRequired(cachedDataToWrite);
}
foreach (var cachedLine in cachedDataToWrite)
{
writer.WriteLine(string.Join(delimiter.ToString(), cachedLine.Value.DataColumns));
}
}
private readonly ITraqIntensityCorrection intensityCorrector = new(
ReporterIons.ReporterIonMassModeConstants.CustomOrNone,
ITraqIntensityCorrection.CorrectionFactorsiTRAQ4Plex.ABSciex);
/// <summary>
/// Looks for the reporter ion m/z values, +/- a tolerance
/// Calls AggregateIonsInRange with returnMax = True, meaning we're reporting the maximum ion abundance for each reporter ion m/z
/// </summary>
/// <param name="rawFileReader"></param>
/// <param name="dataAggregation"></param>
/// <param name="includeFtmsColumns"></param>
/// <param name="sicOptions"></param>
/// <param name="scanList"></param>
/// <param name="spectraCache"></param>
/// <param name="currentScan"></param>
/// <param name="cachedDataToWrite"></param>
/// <param name="reporterIons"></param>
/// <param name="saveUncorrectedIntensities"></param>
/// <param name="saveObservedMasses"></param>
private void FindReporterIonsWork(
XRawFileIO rawFileReader,
DataAggregation dataAggregation,
bool includeFtmsColumns,
SICOptions sicOptions,
ScanList scanList,
SpectraCache spectraCache,
ScanInfo currentScan,
IDictionary<int, ReporterIonStats> cachedDataToWrite,
IList<ReporterIonInfo> reporterIons,
bool saveUncorrectedIntensities,
bool saveObservedMasses)
{
const bool USE_MAX_ABUNDANCE_IN_WINDOW = true;
double parentIonMZ;
if (currentScan.FragScanInfo.ParentIonInfoIndex >= 0 && currentScan.FragScanInfo.ParentIonInfoIndex < scanList.ParentIons.Count)
{
parentIonMZ = scanList.ParentIons[currentScan.FragScanInfo.ParentIonInfoIndex].MZ;
}
else
{
parentIonMZ = 0;
}
if (!spectraCache.GetSpectrum(currentScan.ScanNumber, out var spectrum, true))
{
SetLocalErrorCode(clsMASIC.MasicErrorCodes.ErrorUncachingSpectrum);
return;
}
// Initialize the arrays used to track the observed reporter ion values
var reporterIntensities = new double[reporterIons.Count];
var reporterIntensitiesCorrected = new double[reporterIons.Count];
var closestMZ = new double[reporterIons.Count];
var reporterIonStats = new ReporterIonStats(currentScan.ScanNumber);
// Initialize the output data
reporterIonStats.DataColumns.Add(sicOptions.DatasetID.ToString());
reporterIonStats.DataColumns.Add(currentScan.ScanNumber.ToString());
reporterIonStats.DataColumns.Add(currentScan.FragScanInfo.CollisionMode);
reporterIonStats.DataColumns.Add(StringUtilities.DblToString(parentIonMZ, 2));
reporterIonStats.DataColumns.Add(StringUtilities.DblToString(currentScan.BasePeakIonIntensity, 2));
reporterIonStats.DataColumns.Add(StringUtilities.DblToString(currentScan.BasePeakIonMZ, 4));
reporterIonStats.MSLevel = currentScan.FragScanInfo.MSLevel;
reporterIonStats.ParentIonMz = currentScan.FragScanInfo.ParentIonMz;
if (reporterIonStats.MSLevel <= 2)
{
reporterIonStats.ParentScan = currentScan.FragScanInfo.ParentScan;
// Note that the parent scan is not necessarily the most recent survey scan (i.e., most recent MS1 scan)
}
else
{
reporterIonStats.ParentScan = currentScan.FragScanInfo.ParentScan;
}
reporterIonStats.DataColumns.Add(reporterIonStats.ParentScan.ToString());
var reporterIntensityList = new List<string>(reporterIons.Count);
var obsMZList = new List<string>(reporterIons.Count);
var uncorrectedIntensityList = new List<string>(reporterIons.Count);
var ftmsSignalToNoise = new List<string>(reporterIons.Count);
var ftmsResolution = new List<string>(reporterIons.Count);
//var ftmsLabelDataMz = new List<string>(reporterIons.Count);
double reporterIntensityMax = 0;
// Find the reporter ion intensities
// Also keep track of the closest m/z for each reporter ion
// Note that we're using the maximum intensity in the range (not the sum)
for (var reporterIonIndex = 0; reporterIonIndex < reporterIons.Count; reporterIonIndex++)
{
var ion = reporterIons[reporterIonIndex];
// Search for the reporter ion MZ in this mass spectrum
reporterIntensities[reporterIonIndex] = dataAggregation.AggregateIonsInRange(
spectrum,
ion.MZ,
ion.MZToleranceDa,
out _,
out closestMZ[reporterIonIndex],
USE_MAX_ABUNDANCE_IN_WINDOW);
ion.SignalToNoise = 0;
ion.Resolution = 0;
ion.LabelDataMZ = 0;
}
if (includeFtmsColumns && currentScan.IsHighResolution)
{
// Retrieve the label data for this spectrum
rawFileReader.GetScanLabelData(currentScan.ScanNumber, out var ftLabelData);
// Find each reporter ion in ftLabelData
foreach (var reporterIon in reporterIons)
{
var mzToFind = reporterIon.MZ;
var mzToleranceDa = reporterIon.MZToleranceDa;
var highestIntensity = 0.0;
var udtBestMatch = new FTLabelInfoType();
var matchFound = false;
foreach (var labelItem in ftLabelData)
{
// Compare labelItem.Mass (which is m/z of the ion in labelItem) to the m/z of the current reporter ion
if (Math.Abs(mzToFind - labelItem.Mass) > mzToleranceDa)
{
continue;
}
// m/z is within range
if (labelItem.Intensity > highestIntensity)
{
udtBestMatch = labelItem;
highestIntensity = labelItem.Intensity;
matchFound = true;
}
}
if (matchFound)
{
reporterIon.SignalToNoise = udtBestMatch.SignalToNoise;
reporterIon.Resolution = udtBestMatch.Resolution;
reporterIon.LabelDataMZ = udtBestMatch.Mass;
}
}
}
// Populate reporterIntensitiesCorrected with the data in reporterIntensities
Array.Copy(reporterIntensities, reporterIntensitiesCorrected, reporterIntensities.Length);
if (mOptions.ReporterIons.ReporterIonApplyAbundanceCorrection)
{
if (mOptions.ReporterIons.ReporterIonMassMode is
ReporterIons.ReporterIonMassModeConstants.ITraqFourMZ or
ReporterIons.ReporterIonMassModeConstants.ITraqEightMZHighRes or
ReporterIons.ReporterIonMassModeConstants.ITraqEightMZLowRes or
ReporterIons.ReporterIonMassModeConstants.TMTTenMZ or
ReporterIons.ReporterIonMassModeConstants.TMTElevenMZ or
ReporterIons.ReporterIonMassModeConstants.TMTSixteenMZ or
ReporterIons.ReporterIonMassModeConstants.TMTEighteenMZ)
{
// Correct the reporter ion intensities using the Reporter Ion Intensity Corrector class
if (intensityCorrector.ReporterIonMode != mOptions.ReporterIons.ReporterIonMassMode ||
intensityCorrector.ITraq4PlexCorrectionFactorType != mOptions.ReporterIons.ReporterIonITraq4PlexCorrectionFactorType)
{
intensityCorrector.UpdateReporterIonMode(
mOptions.ReporterIons.ReporterIonMassMode,
mOptions.ReporterIons.ReporterIonITraq4PlexCorrectionFactorType);
}
// Count the number of non-zero data points in reporterIntensitiesCorrected()
var positiveCount = 0;
for (var reporterIonIndex = 0; reporterIonIndex < reporterIons.Count; reporterIonIndex++)
{
if (reporterIntensitiesCorrected[reporterIonIndex] > 0)
{
positiveCount++;
}
}
// Apply the correction if 2 or more points are non-zero
if (positiveCount >= 2)
{
intensityCorrector.ApplyCorrection(reporterIntensitiesCorrected);
}
}
}
// Now construct the string of intensity values, delimited by delimiter
// Will also compute the percent change in intensities
// Initialize the variables used to compute the weighted average percent change
double pctChangeSum = 0;
double originalIntensitySum = 0;
for (var reporterIonIndex = 0; reporterIonIndex < reporterIons.Count; reporterIonIndex++)
{
if (!reporterIons[reporterIonIndex].ContaminantIon)
{
// Update the PctChange variables and the IntensityMax variable only if this is not a Contaminant Ion
originalIntensitySum += reporterIntensities[reporterIonIndex];
if (reporterIntensities[reporterIonIndex] > 0)
{
// Compute the percent change, update pctChangeSum
var pctChange =
(reporterIntensitiesCorrected[reporterIonIndex] - reporterIntensities[reporterIonIndex]) /
reporterIntensities[reporterIonIndex];
// Using Absolute Value here to prevent negative changes from canceling out positive changes
pctChangeSum += Math.Abs(pctChange * reporterIntensities[reporterIonIndex]);
}
if (reporterIntensitiesCorrected[reporterIonIndex] > reporterIntensityMax)
{
reporterIntensityMax = reporterIntensitiesCorrected[reporterIonIndex];
}
}
if (!reporterIons[reporterIonIndex].ContaminantIon || saveUncorrectedIntensities)
{
// Append the reporter ion intensity to reporterIntensityList
// We skip contaminant ions, unless saveUncorrectedIntensities is True, in which case we include them
reporterIntensityList.Add(
reporterIntensitiesCorrected[reporterIonIndex] < float.Epsilon
? "0"
: StringUtilities.DblToString(reporterIntensitiesCorrected[reporterIonIndex], 2));
if (saveObservedMasses)
{
// Append the observed reporter mass value to obsMZList
obsMZList.Add(StringUtilities.DblToString(closestMZ[reporterIonIndex], 3));
}
if (saveUncorrectedIntensities)
{
// Append the original, uncorrected intensity value
uncorrectedIntensityList.Add(
reporterIntensities[reporterIonIndex] < float.Epsilon
? "0"
: StringUtilities.DblToString(reporterIntensities[reporterIonIndex], 2));
}
if (!includeFtmsColumns)
continue;
if (Math.Abs(reporterIons[reporterIonIndex].SignalToNoise) < float.Epsilon &&
Math.Abs(reporterIons[reporterIonIndex].Resolution) < float.Epsilon &&
Math.Abs(reporterIons[reporterIonIndex].LabelDataMZ) < float.Epsilon)
{
// A match was not found in the label data; display blanks (not zeros)
ftmsSignalToNoise.Add(string.Empty);
ftmsResolution.Add(string.Empty);
//ftmsLabelDataMz.Add(string.Empty);
}
else
{
ftmsSignalToNoise.Add(StringUtilities.DblToString(reporterIons[reporterIonIndex].SignalToNoise, 2));
ftmsResolution.Add(StringUtilities.DblToString(reporterIons[reporterIonIndex].Resolution, 2));
//ftmsLabelDataMz.Add(StringUtilities.DblToString(reporterIons(reporterIonIndex).LabelDataMZ, 4));
}
}
}
// Compute the weighted average percent intensity correction value
// This will be a value between 0 and 100
float weightedAvgPctIntensityCorrection;
if (originalIntensitySum > 0)
{
weightedAvgPctIntensityCorrection = (float)(pctChangeSum / originalIntensitySum * 100);
}
else
{
weightedAvgPctIntensityCorrection = 0;
}
// Resize the target list capacity to large enough to hold all data.
reporterIonStats.DataColumns.Capacity =
reporterIntensityList.Count + 3 +
obsMZList.Count + uncorrectedIntensityList.Count +
ftmsSignalToNoise.Count + ftmsResolution.Count;
// Append the maximum reporter ion intensity, then the individual reporter ion intensities
reporterIonStats.DataColumns.Add(StringUtilities.DblToString(reporterIntensityMax, 2));
reporterIonStats.ReporterIonIntensityStartIndex = reporterIonStats.DataColumns.Count;
reporterIonStats.ReporterIonIntensityEndIndex = reporterIonStats.ReporterIonIntensityStartIndex + reporterIntensityList.Count - 1;
reporterIonStats.DataColumns.AddRange(reporterIntensityList);
// Append the weighted average percent intensity correction
reporterIonStats.DataColumns.Add(
weightedAvgPctIntensityCorrection < float.Epsilon
? "0"
: StringUtilities.DblToString(weightedAvgPctIntensityCorrection, 1));
if (saveObservedMasses)
{
reporterIonStats.DataColumns.AddRange(obsMZList);
}
if (saveUncorrectedIntensities)
{
reporterIonStats.DataColumns.AddRange(uncorrectedIntensityList);
}
if (includeFtmsColumns)
{
reporterIonStats.DataColumns.AddRange(ftmsSignalToNoise);
reporterIonStats.DataColumns.AddRange(ftmsResolution);
// Uncomment to include the label data m/z value in the _ReporterIons.txt file
//if (saveObservedMasses)
// reporterIonStats.DataColumns.AddRange(ftmsLabelDataMz)
}
cachedDataToWrite.Add(currentScan.ScanNumber, reporterIonStats);
}
/// <summary>
/// Compute the median reporter ion value
/// </summary>
/// <param name="scanDescription"></param>
/// <param name="reporterIonIntensities"></param>
/// <param name="medianIgnoringZeros">Median value, ignoring zeros</param>
/// <returns>Median value, including zeros</returns>
private double GetMedianReporterIonIntensity(string scanDescription, List<string> reporterIonIntensities, out double medianIgnoringZeros)
{
var reporterIonIntensityValues = new List<double>();
var nonZeroIntensities = new List<double>();
var validNumbers = 0;
foreach (var item in reporterIonIntensities)
{
if (!double.TryParse(item, out var reporterIonIntensity))
{
reporterIonIntensityValues.Add(0);
continue;
}
validNumbers++;
reporterIonIntensityValues.Add(reporterIonIntensity);
if (reporterIonIntensity > 0)
nonZeroIntensities.Add(reporterIonIntensity);
}
if (validNumbers == 0)
{
OnWarningEvent("No valid reporter ions were found in {0}", scanDescription);
medianIgnoringZeros = 0;
return 0;
}
medianIgnoringZeros = GetMedianValue(scanDescription + " (non-zero values)", nonZeroIntensities);
return GetMedianValue(scanDescription + " (all values)", reporterIonIntensityValues);
}
/// <summary>
/// Compute the median value for a list of doubles
/// </summary>
/// <param name="scanDescription"></param>
/// <param name="values"></param>
/// <returns>Median value, or 0 if an empty list or the computed median is NaN</returns>
private double GetMedianValue(string scanDescription, IReadOnlyCollection<double> values)
{
if (values.Count == 0)
return 0;
var medianValue = values.Median();
if (!double.IsNaN(medianValue))
return medianValue;
OnWarningEvent("Median reporter ion intensity is NaN for {0}", scanDescription);
return 0;
}
/// <summary>
/// Reporter ion info comparison class
/// </summary>
/// <remarks>Compares m/z values</remarks>
protected class ReportIonInfoComparer : IComparer<ReporterIonInfo>
{
/// <summary>
/// Compare the m/z values of two reporter ions
/// </summary>
/// <param name="x"></param>
/// <param name="y"></param>
/// <returns>-1, 0, or 1</returns>
public int Compare(ReporterIonInfo x, ReporterIonInfo y)
{
var reporterIonInfoA = x;
var reporterIonInfoB = y;
if (reporterIonInfoA == null || reporterIonInfoB == null)
return 0;
if (reporterIonInfoA.MZ > reporterIonInfoB.MZ)
{
return 1;
}
if (reporterIonInfoA.MZ < reporterIonInfoB.MZ)
{
return -1;
}
return 0;
}
}
}
}