public void TestGetScanCountsByScanType(
string uimfFileName,
int frameStart,
int frameEnd,
int expectedMS1,
int expectedMS2,
int expectedTotalScanCount)
{
var dataFile = GetUimfDataFile(uimfFileName);
using (var reader = new MSDataFileReader(dataFile.FullName))
{
Console.WriteLine("Parsing scan headers for {0}", dataFile.Name);
var scanCount = reader.SpectrumCount;
Console.WriteLine("Total scans: {0}", scanCount);
Assert.AreEqual(expectedTotalScanCount, scanCount, "Total scan count mismatch");
Console.WriteLine();
var frameScanPairToIndexMap = reader.GetUimfFrameScanPairToIndexMapping();
var scanCountMS1 = 0;
var scanCountMS2 = 0;
foreach (var frame in frameScanPairToIndexMap)
{
var frameNumber = frame.Key.Key;
var scanNumber = frame.Key.Value;
var spectrumIndex = frame.Value;
if (frameNumber < frameStart || frameNumber > frameEnd)
{
continue;
}
var spectrum = reader.GetSpectrum(spectrumIndex, false);
if (spectrum.Level > 1)
{
scanCountMS2++;
}
else
{
scanCountMS1++;
}
}
Console.WriteLine("scanCountMS1={0}", scanCountMS1);
Console.WriteLine("scanCountMS2={0}", scanCountMS2);
Assert.AreEqual(expectedMS1, scanCountMS1, "MS1 scan count mismatch");
Assert.AreEqual(expectedMS2, scanCountMS2, "MS2 scan count mismatch");
}
}
public void TestGetScanCountsByScanType(
string dotDFolderName,
int scanStart,
int scanEnd,
int expectedMS1,
int expectedMS2,
int expectedTotalScanCount)
{
var dataFolder = GetBrukerDataFolder(dotDFolderName);
using (var reader = new MSDataFileReader(dataFolder.FullName))
{
Console.WriteLine("Parsing scan headers for {0}", dataFolder.Name);
var scanCount = reader.SpectrumCount;
Console.WriteLine("Total scans: {0}", scanCount);
Assert.AreEqual(expectedTotalScanCount, scanCount, "Total scan count mismatch");
Console.WriteLine();
var scanNumberToIndexMap = reader.GetScanToIndexMapping();
var scanCountMS1 = 0;
var scanCountMS2 = 0;
foreach (var scan in scanNumberToIndexMap.Where(x => x.Key >= scanStart && x.Key <= scanEnd))
{
// var scanNumber = scan.Key;
var spectrumIndex = scan.Value;
var spectrum = reader.GetSpectrum(spectrumIndex, false);
if (spectrum.Level > 1)
{
scanCountMS2++;
}
else
{
scanCountMS1++;
}
}
Console.WriteLine("scanCountMS1={0}", scanCountMS1);
Console.WriteLine("scanCountMS2={0}", scanCountMS2);
Assert.AreEqual(expectedMS1, scanCountMS1, "MS1 scan count mismatch");
Assert.AreEqual(expectedMS2, scanCountMS2, "MS2 scan count mismatch");
}
}
public MzRun(string fileName)
: this()
{
var fileInfo = new FileInfo(fileName);
if (!fileInfo.Exists)
{
throw new FileNotFoundException("Cannot initialize Run. File not found: " + fileName);
}
var fileExtension = Path.GetExtension(fileName).ToLower();
switch (fileExtension)
{
case ".mzxml":
MSFileType = Globals.MSFileType.MZXML_Rawdata;
break;
case ".mzml":
MSFileType = Globals.MSFileType.MZML;
break;
case ".mz5":
MSFileType = Globals.MSFileType.MZ5;
break;
default:
throw new IOException("Cannot initialize Run. File extension " + fileExtension + " isn't supported. The following file extensions are supported: mzXML, mzML, and mz5");
}
Filename = fileName;
var baseFilename = Path.GetFileName(Filename);
DatasetName = baseFilename.Substring(0, baseFilename.LastIndexOf('.'));
DataSetPath = Path.GetDirectoryName(Filename);
_reader = new MSDataFileReader(fileName);
MinLCScan = GetMinPossibleLCScanNum();
MaxLCScan = GetMaxPossibleLCScanNum();
}
/// <summary>
/// Constructor
/// </summary>
/// <param name="pWiz"></param>
/// <param name="datasetStatsSummarizer"></param>
/// <param name="ticAndBPIPlot"></param>
/// <param name="lcms2DPlot"></param>
/// <param name="saveLCMS2DPlots"></param>
/// <param name="saveTICAndBPI"></param>
/// <param name="checkCentroidingStatus"></param>
public clsProteoWizardDataParser(
MSDataFileReader pWiz,
DatasetStatsSummarizer datasetStatsSummarizer,
clsTICandBPIPlotter ticAndBPIPlot,
clsLCMSDataPlotter lcms2DPlot,
bool saveLCMS2DPlots,
bool saveTICAndBPI,
bool checkCentroidingStatus)
{
mPWiz = pWiz;
mDatasetStatsSummarizer = datasetStatsSummarizer;
mTICAndBPIPlot = ticAndBPIPlot;
mLCMS2DPlot = lcms2DPlot;
mSaveLCMS2DPlots = saveLCMS2DPlots;
mSaveTICAndBPI = saveTICAndBPI;
mCheckCentroidingStatus = checkCentroidingStatus;
mGetQ1MZ = new Regex("Q[0-9]=([0-9.]+)", RegexOptions.Compiled);
mGetQ3MZ = new Regex("Q1=[0-9.]+ Q3=([0-9.]+)", RegexOptions.Compiled);
mWarnedAccessViolationException = false;
}
public void TestPWiz(
string fileOrDirectoryName,
bool isDirectory,
int expectedSpectraInFile,
int expectedSpectraLoaded,
int expectedTotalDataPoints,
double expectedMedianTIC,
double expectedMedianBPI)
{
try
{
if (!InstrumentDataUtilities.FindInstrumentData(fileOrDirectoryName, isDirectory, out var instrumentDataFileOrDirectory))
{
Assert.Fail("File or directory not found");
return;
}
using (var reader = new MSDataFileReader(instrumentDataFileOrDirectory.FullName))
{
Console.WriteLine("Chromatogram count: " + reader.ChromatogramCount);
Console.WriteLine();
var ticIntensities = new Dictionary <int, float>();
for (var chromatogramIndex = 0; chromatogramIndex < reader.ChromatogramCount; chromatogramIndex++)
{
// Note that even for a small .Wiff file (1.5 MB), obtaining the Chromatogram list will take some time (20 to 60 seconds)
// The chromatogram at index 0 should be the TIC
// The chromatogram at index >=1 will be each SRM
reader.GetChromatogram(chromatogramIndex, out var chromatogramID, out var timeArray, out var intensityArray);
// Determine the chromatogram type
if (chromatogramID == null)
{
chromatogramID = string.Empty;
}
var cvParams = reader.GetChromatogramCVParams(chromatogramIndex);
if (MSDataFileReader.TryGetCVParamDouble(cvParams, pwiz.CLI.cv.CVID.MS_TIC_chromatogram, out _))
{
// This chromatogram is the TIC
Console.WriteLine("TIC has id {0} and {1} data points", chromatogramID, timeArray.Length);
for (var i = 0; i < intensityArray.Length; i++)
{
ticIntensities.Add(i, intensityArray[i]);
}
}
if (MSDataFileReader.TryGetCVParamDouble(cvParams, pwiz.CLI.cv.CVID.MS_selected_reaction_monitoring_chromatogram, out _))
{
// This chromatogram is an SRM scan
Console.WriteLine("SRM scan has id {0} and {1} data points", chromatogramID, timeArray.Length);
}
}
Console.WriteLine("Spectrum count: " + reader.SpectrumCount);
var spectraLoaded = 0;
long totalPointsRead = 0;
double ticSumAllSpectra = 0;
double bpiSumAllSpectra = 0;
var spectrumIndex = 0;
while (spectrumIndex < reader.SpectrumCount)
{
var spectrum = reader.GetSpectrum(spectrumIndex, getBinaryData: true);
spectraLoaded += 1;
Console.WriteLine();
Console.WriteLine("ScanIndex {0}, NativeId {1}, Elution Time {2:F2} minutes, MS Level {3}",
spectrumIndex, spectrum.NativeId, spectrum.RetentionTime, spectrum.Level);
// Use the following to get the MZs and Intensities
var mzList = spectrum.Mzs.ToList();
var intensities = spectrum.Intensities.ToList();
if (mzList.Count > 0)
{
Console.WriteLine(" Data count: " + mzList.Count);
totalPointsRead += mzList.Count;
double tic = 0;
double bpi = 0;
for (var index = 0; index <= mzList.Count - 1; index++)
{
tic += intensities[index];
if (intensities[index] > bpi)
{
bpi = intensities[index];
}
}
ticSumAllSpectra += tic;
bpiSumAllSpectra += bpi;
if (!ticIntensities.TryGetValue(spectrumIndex, out var ticFromChromatogram))
{
ticFromChromatogram = -1;
}
var spectrumInfo = reader.GetSpectrumObject(spectrumIndex);
if (MSDataFileReader.TryGetCVParamDouble(spectrumInfo.cvParams, pwiz.CLI.cv.CVID.MS_total_ion_current,
out var ticFromSpectrumObject))
{
if (ticFromChromatogram < 0)
{
// ticIntensities did not have an entry for spectrumIndex
// This could be the case on a Waters Synapt instrument, where ticIntensities has one TIC per frame,
// while pWiz.GetSpectrum() returns individual mass spectra, of which there could be hundreds of spectra per frame
Console.WriteLine(" TIC from actual data is {0:E2} vs. {1:E2} from the spectrum object",
tic, ticFromSpectrumObject);
}
else
{
// Note: the TIC value from the CvParams has been seen to be drastically off from the manually computed value
Console.WriteLine(
" TIC from actual data is {0:E2} vs. {1:E2} from the chromatogram and {2:E2} from the spectrum object",
tic, ticFromChromatogram, ticFromSpectrumObject);
}
}
if (MSDataFileReader.TryGetCVParamDouble(spectrumInfo.cvParams, pwiz.CLI.cv.CVID.MS_base_peak_intensity,
out var bpiFromSpectrumObject))
{
if (MSDataFileReader.TryGetCVParamDouble(spectrumInfo.cvParams, pwiz.CLI.cv.CVID.MS_base_peak_m_z,
out var bpiMzFromSpectrumObject))
{
// Note: the BPI intensity from the CvParams has been seen to be drastically off from the manually computed value
Console.WriteLine(" BPI from spectrum object is {0:E2} at {1:F3} m/z",
bpiFromSpectrumObject, bpiMzFromSpectrumObject);
}
}
}
if (spectrumIndex < 25)
{
spectrumIndex += 1;
}
else if (spectrumIndex < 1250)
{
spectrumIndex += 50;
}
else
{
spectrumIndex += 500;
}
}
if (spectraLoaded > 0)
{
var medianTIC = ticSumAllSpectra / spectraLoaded;
var medianBPI = bpiSumAllSpectra / spectraLoaded;
Console.WriteLine();
Console.WriteLine("Read {0:N0} data points from {1} spectra in {2}",
totalPointsRead, spectraLoaded, Path.GetFileName(fileOrDirectoryName));
Console.WriteLine("Median TIC: {0:E4}", medianTIC);
Console.WriteLine("Median BPI: {0:E4}", medianBPI);
Assert.AreEqual(expectedSpectraInFile, reader.SpectrumCount, "Total spectrum count mismatch");
Assert.AreEqual(expectedSpectraLoaded, spectraLoaded, "Spectra loaded mismatch");
Assert.AreEqual(expectedTotalDataPoints, totalPointsRead, "Spectra loaded mismatch");
var ticComparisonTolerance = expectedMedianTIC * 0.01;
var bpiComparisonTolerance = expectedMedianBPI * 0.01;
Assert.AreEqual(expectedMedianTIC, medianTIC, ticComparisonTolerance, "Median TIC mismatch");
Assert.AreEqual(expectedMedianBPI, medianBPI, bpiComparisonTolerance, "Median BPI mismatch");
}
}
}
catch (Exception ex)
{
ConsoleMsgUtils.ShowError("Error using ProteoWizard reader", ex);
}
}
public bool StoreMSSpectraInfo(
bool ticStored,
ref double runtimeMinutes,
bool skipExistingScans,
bool skipScansWithNoIons,
int maxScansToTrackInDetail,
int maxScansForTicAndBpi,
out int scanCountSuccess,
out int scanCountError)
{
scanCountSuccess = 0;
scanCountError = 0;
try
{
Console.WriteLine();
OnStatusEvent("Obtaining scan times and MSLevels (this could take several minutes)");
mLastScanLoadingDebugProgressTime = DateTime.UtcNow;
mLastScanLoadingStatusProgressTime = DateTime.UtcNow;
mReportedTotalSpectraToExamine = false;
mCancellationToken = new CancellationTokenSource();
var scanTimes = new double[0];
var msLevels = new byte[0];
mGetScanTimesStartTime = DateTime.UtcNow;
mGetScanTimesMaxWaitTimeSeconds = 90;
mGetScanTimesAutoAborted = false;
var minScanIndexWithoutScanTimes = int.MaxValue;
try
{
mPWiz.GetScanTimesAndMsLevels(mCancellationToken.Token, out scanTimes, out msLevels, MonitorScanTimeLoadingProgress);
}
catch (OperationCanceledException)
{
// mCancellationToken.Cancel was called in MonitorScanTimeLoadingProgress
// Determine the scan index where GetScanTimesAndMsLevels exited the for loop
for (var scanIndex = 0; scanIndex <= scanTimes.Length - 1; scanIndex++)
{
if (msLevels[scanIndex] > 0)
{
continue;
}
minScanIndexWithoutScanTimes = scanIndex;
break;
}
if (!mGetScanTimesAutoAborted && minScanIndexWithoutScanTimes < int.MaxValue)
{
// Manually aborted; shrink the arrays to reflect the amount of data that was actually loaded
Array.Resize(ref scanTimes, minScanIndexWithoutScanTimes);
Array.Resize(ref msLevels, minScanIndexWithoutScanTimes);
}
}
var spectrumCount = scanTimes.Length;
// The scan times returned by .GetScanTimesAndMsLevels() are the acquisition time in seconds from the start of the analysis
// Convert these to minutes
for (var scanIndex = 0; scanIndex <= spectrumCount - 1; scanIndex++)
{
if (scanIndex >= minScanIndexWithoutScanTimes)
{
break;
}
var scanTimeMinutes = scanTimes[scanIndex] / 60.0;
scanTimes[scanIndex] = scanTimeMinutes;
}
Console.WriteLine();
OnStatusEvent("Reading spectra");
var lastDebugProgressTime = DateTime.UtcNow;
var lastStatusProgressTime = DateTime.UtcNow;
var skippedEmptyScans = 0;
var scanNumber = 0;
var scansStored = 0;
var ticAndBpiScansStored = 0;
var scanCountHMS = 0;
var scanCountHMSn = 0;
var scanCountMS = 0;
var scanCountMSn = 0;
for (var scanIndex = 0; scanIndex <= spectrumCount - 1; scanIndex++)
{
try
{
var computeTIC = true;
var computeBPI = true;
// Obtain the raw mass spectrum
var msDataSpectrum = mPWiz.GetSpectrum(scanIndex);
scanNumber = scanIndex + 1;
if (scanIndex >= minScanIndexWithoutScanTimes)
{
// msDataSpectrum.RetentionTime is already in minutes
scanTimes[scanIndex] = msDataSpectrum.RetentionTime ?? 0;
if (msDataSpectrum.Level >= byte.MinValue && msDataSpectrum.Level <= byte.MaxValue)
{
msLevels[scanIndex] = (byte)msDataSpectrum.Level;
}
}
var scanStatsEntry = new ScanStatsEntry
{
ScanNumber = scanNumber,
ScanType = msDataSpectrum.Level
};
if (msLevels[scanIndex] > 1)
{
if (HighResMS2)
{
scanStatsEntry.ScanTypeName = "HMSn";
scanCountHMSn++;
}
else
{
scanStatsEntry.ScanTypeName = "MSn";
scanCountMSn++;
}
}
else
{
if (HighResMS1)
{
scanStatsEntry.ScanTypeName = "HMS";
scanCountHMS++;
}
else
{
scanStatsEntry.ScanTypeName = "MS";
scanCountMS++;
}
}
var driftTimeMsec = msDataSpectrum.DriftTimeMsec ?? 0;
scanStatsEntry.ScanFilterText = driftTimeMsec > 0 ? "IMS" : string.Empty;
scanStatsEntry.ExtendedScanInfo.ScanFilterText = scanStatsEntry.ScanFilterText;
scanStatsEntry.DriftTimeMsec = driftTimeMsec.ToString("0.0###");
scanStatsEntry.ElutionTime = scanTimes[scanIndex].ToString("0.0###");
// Bump up runtimeMinutes if necessary
if (scanTimes[scanIndex] > runtimeMinutes)
{
runtimeMinutes = scanTimes[scanIndex];
}
var spectrum = mPWiz.GetSpectrumObject(scanIndex);
if (MSDataFileReader.TryGetCVParamDouble(spectrum.cvParams, pwiz.CLI.cv.CVID.MS_total_ion_current, out var tic))
{
// For timsTOF data, this is the TIC of the entire frame
scanStatsEntry.TotalIonIntensity = StringUtilities.ValueToString(tic, 5);
computeTIC = false;
}
if (MSDataFileReader.TryGetCVParamDouble(spectrum.cvParams, pwiz.CLI.cv.CVID.MS_base_peak_intensity, out var bpi))
{
// For timsTOF data, this is the BPI of the entire frame
// Additionally, for timsTOF data, MS_base_peak_m_z is not defined
scanStatsEntry.BasePeakIntensity = StringUtilities.ValueToString(bpi, 5);
if (MSDataFileReader.TryGetCVParamDouble(spectrum.scanList.scans[0].cvParams, pwiz.CLI.cv.CVID.MS_base_peak_m_z, out var basePeakMzFromCvParams))
{
scanStatsEntry.BasePeakMZ = StringUtilities.ValueToString(basePeakMzFromCvParams, 5);
computeBPI = false;
}
}
if (string.IsNullOrEmpty(scanStatsEntry.ScanFilterText))
{
if (spectrum?.scanList?.scans.Count > 0)
{
// Bruker timsTOF datasets will have CVParam "inverse reduced ion mobility" for IMS spectra; check for this
foreach (var scanItem in spectrum.scanList.scans)
{
if (MSDataFileReader.TryGetCVParam(scanItem.cvParams, pwiz.CLI.cv.CVID.MS_inverse_reduced_ion_mobility, out _))
{
scanStatsEntry.ScanFilterText = "IMS";
break;
}
}
}
}
// Base peak signal to noise ratio
scanStatsEntry.BasePeakSignalToNoiseRatio = "0";
scanStatsEntry.IonCount = msDataSpectrum.Mzs.Length;
scanStatsEntry.IonCountRaw = scanStatsEntry.IonCount;
if ((computeBPI || computeTIC) && scanStatsEntry.IonCount > 0)
{
// Step through the raw data to compute the BPI and TIC
var mzList = msDataSpectrum.Mzs;
var intensities = msDataSpectrum.Intensities;
tic = 0;
bpi = 0;
double basePeakMZ = 0;
for (var index = 0; index <= mzList.Length - 1; index++)
{
tic += intensities[index];
if (intensities[index] > bpi)
{
bpi = intensities[index];
basePeakMZ = mzList[index];
}
}
scanStatsEntry.TotalIonIntensity = StringUtilities.ValueToString(tic, 5);
scanStatsEntry.BasePeakIntensity = StringUtilities.ValueToString(bpi, 5);
scanStatsEntry.BasePeakMZ = StringUtilities.ValueToString(basePeakMZ, 5);
}
var addScan = !skipExistingScans || skipExistingScans && !mDatasetStatsSummarizer.HasScanNumber(scanNumber);
if (addScan)
{
if (skipScansWithNoIons && scanStatsEntry.IonCount == 0)
{
skippedEmptyScans++;
if (skippedEmptyScans < 25 ||
skippedEmptyScans < 100 && skippedEmptyScans % 10 == 0 ||
skippedEmptyScans < 1000 && skippedEmptyScans % 100 == 0 ||
skippedEmptyScans < 10000 && skippedEmptyScans % 1000 == 0 ||
skippedEmptyScans < 100000 && skippedEmptyScans % 10000 == 0 ||
skippedEmptyScans % 100000 == 0)
{
ConsoleMsgUtils.ShowDebug("Skipping scan {0:N0} since no ions; {1:N0} total skipped scans", scanNumber, skippedEmptyScans);
}
}
else
{
if (maxScansToTrackInDetail < 0 || scansStored < maxScansToTrackInDetail)
{
mDatasetStatsSummarizer.AddDatasetScan(scanStatsEntry);
scansStored += 1;
}
}
}
if (mSaveTICAndBPI && !ticStored && (maxScansForTicAndBpi < 0 || ticAndBpiScansStored < maxScansForTicAndBpi))
{
mTICAndBPIPlot.AddData(scanStatsEntry.ScanNumber, msLevels[scanIndex], (float)scanTimes[scanIndex], bpi, tic);
ticAndBpiScansStored += 1;
}
if (mSaveLCMS2DPlots && addScan)
{
mLCMS2DPlot.AddScan(scanStatsEntry.ScanNumber, msLevels[scanIndex], (float)scanTimes[scanIndex], msDataSpectrum.Mzs.Length, msDataSpectrum.Mzs, msDataSpectrum.Intensities);
}
if (mCheckCentroidingStatus)
{
mDatasetStatsSummarizer.ClassifySpectrum(msDataSpectrum.Mzs, msLevels[scanIndex], "Scan " + scanStatsEntry.ScanNumber);
}
scanCountSuccess += 1;
}
catch (Exception ex)
{
OnErrorEvent("Error loading header info for scan " + scanNumber, ex);
scanCountError += 1;
}
if (DateTime.UtcNow.Subtract(lastStatusProgressTime).TotalMinutes > 5)
{
OnStatusEvent(string.Format("Reading spectra, loaded {0:N0} / {1:N0} spectra; " +
"{2:N0} HMS spectra; {3:N0} HMSn spectra; " +
"{4:N0} MS spectra; {5:N0} MSn spectra; " +
"max elution time is {6:F2} minutes",
scanNumber, spectrumCount,
scanCountHMS, scanCountHMSn,
scanCountMS, scanCountMSn,
runtimeMinutes));
lastStatusProgressTime = DateTime.UtcNow;
lastDebugProgressTime = DateTime.UtcNow;
continue;
}
if (DateTime.UtcNow.Subtract(lastDebugProgressTime).TotalSeconds < 15)
{
continue;
}
lastDebugProgressTime = DateTime.UtcNow;
var percentComplete = scanNumber / (float)spectrumCount * 100;
var percentCompleteOverall = clsMSFileInfoProcessorBaseClass.ComputeIncrementalProgress(
PROGRESS_SCAN_TIMES_LOADED,
clsMSFileInfoProcessorBaseClass.PROGRESS_SPECTRA_LOADED,
percentComplete);
OnProgressUpdate(string.Format("Spectra processed: {0:N0}", scanNumber), percentCompleteOverall);
}
mDatasetStatsSummarizer.StoreScanTypeTotals(scanCountHMS, scanCountHMSn,
scanCountMS, scanCountMSn,
runtimeMinutes);
var scanCountTotal = scanCountSuccess + scanCountError;
if (scanCountTotal == 0)
{
return(false);
}
// Return True if at least 50% of the spectra were successfully read
return(scanCountSuccess >= scanCountTotal / 2.0);
}
catch (AccessViolationException)
{
// Attempted to read or write protected memory. This is often an indication that other memory is corrupt.
if (!mWarnedAccessViolationException)
{
OnWarningEvent("Error reading instrument data with ProteoWizard: Attempted to read or write protected memory. " +
"The instrument data file is likely corrupt.");
mWarnedAccessViolationException = true;
}
mDatasetStatsSummarizer.CreateEmptyScanStatsFiles = false;
return(false);
}
catch (Exception ex)
{
OnErrorEvent("Error reading instrument data with ProteoWizard: " + ex.Message, ex);
return(false);
}
}
public void StoreChromatogramInfo(DatasetFileInfo datasetFileInfo, out bool ticStored, out bool srmDataCached, out double runtimeMinutes)
{
var ticScanTimes = new List <float>();
var ticScanNumbers = new List <int>();
// This dictionary tracks the m/z and intensity values for parent (Q1) ions of each scan
// Key is ScanNumber; Value is a dictionary holding m/z and intensity values for that scan
var dct2DDataParent = new Dictionary <int, Dictionary <double, double> >();
// This dictionary tracks the m/z and intensity values for product (Q3) ions of each scan
var dct2DDataProduct = new Dictionary <int, Dictionary <double, double> >();
// This dictionary tracks the scan times for each scan number tracked by dct2DDataParent and/or dct2DDataProduct
var dct2DDataScanTimes = new Dictionary <int, float>();
// Note that even for a small .Wiff file (1.5 MB), obtaining the first chromatogram will take some time (20 to 60 seconds)
// The chromatogram at index 0 should be the TIC
// The chromatogram at index >=1 will be each SRM
runtimeMinutes = 0;
ticStored = false;
srmDataCached = false;
for (var chromatogramIndex = 0; chromatogramIndex <= mPWiz.ChromatogramCount - 1; chromatogramIndex++)
{
try
{
if (chromatogramIndex == 0)
{
OnStatusEvent("Obtaining chromatograms (this could take as long as 60 seconds)");
}
mPWiz.GetChromatogram(chromatogramIndex, out var chromatogramID, out var scanTimes, out var intensities);
if (chromatogramID == null)
{
chromatogramID = string.Empty;
}
var cvParams = mPWiz.GetChromatogramCVParams(chromatogramIndex);
if (MSDataFileReader.TryGetCVParam(cvParams, pwiz.CLI.cv.CVID.MS_TIC_chromatogram, out _))
{
// This chromatogram is the TIC
var storeInTICAndBPIPlot = (mSaveTICAndBPI && mPWiz.SpectrumCount == 0);
ProcessTIC(scanTimes, intensities, ticScanTimes, ticScanNumbers, ref runtimeMinutes, storeInTICAndBPIPlot);
ticStored = storeInTICAndBPIPlot;
// This is FrameCount for Bruker timsTOF datasets
datasetFileInfo.ScanCount = scanTimes.Length;
}
if (MSDataFileReader.TryGetCVParam(cvParams, pwiz.CLI.cv.CVID.MS_selected_reaction_monitoring_chromatogram, out _))
{
// This chromatogram is an SRM scan
ProcessSRM(chromatogramID, scanTimes, intensities, ticScanTimes, ticScanNumbers, ref runtimeMinutes, dct2DDataParent,
dct2DDataProduct, dct2DDataScanTimes);
srmDataCached = true;
}
}
catch (AccessViolationException)
{
// Attempted to read or write protected memory. This is often an indication that other memory is corrupt.
if (!mWarnedAccessViolationException)
{
OnWarningEvent("Error loading chromatogram data with ProteoWizard: Attempted to read or write protected memory. " +
"The instrument data file is likely corrupt.");
mWarnedAccessViolationException = true;
}
mDatasetStatsSummarizer.CreateEmptyScanStatsFiles = false;
}
catch (Exception ex)
{
OnErrorEvent("Error processing chromatogram " + chromatogramIndex + " with ProteoWizard: " + ex.Message, ex);
}
}
if (!mSaveLCMS2DPlots)
{
return;
}
if (dct2DDataParent.Count <= 0 && dct2DDataProduct.Count <= 0)
{
return;
}
// Now that all of the chromatograms have been processed, transfer data from dct2DDataParent and dct2DDataProduct into mLCMS2DPlot
mLCMS2DPlot.Options.MS1PlotTitle = "Q1 m/z";
mLCMS2DPlot.Options.MS2PlotTitle = "Q3 m/z";
Store2DPlotData(dct2DDataScanTimes, dct2DDataParent, dct2DDataProduct);
}
public void TestGetScanData(string dotDFolderName, int scanStart, int scanEnd)
{
var expectedData = new Dictionary <string, Dictionary <int, string> >();
// Keys in this dictionary are the scan number of data being retrieved
var file1Data = new Dictionary <int, string>
{
{ 5, "5 39775 39775 982.741 0.0E+0 1410.843 8.7E+4" },
{ 6, "6 39775 39775 982.741 0.0E+0 1410.843 9.1E+4" },
{ 7, "7 39775 39775 982.741 0.0E+0 1410.843 8.7E+4" },
{ 8, "8 39775 39775 982.741 0.0E+0 1410.843 4.5E+4" },
{ 9, "9 39775 39775 982.741 0.0E+0 1410.843 1.4E+5" }
};
expectedData.Add("Humira_100fmol_20121026_hi_res_9_01_716", file1Data);
var file2Data = new Dictionary <int, string>
{
{ 1, "1 7615807 7615807 110.561 3.8E+4 202.468 4.2E+5" }
};
expectedData.Add("Blank-2_05May16_Leopard_Infuse_1_01_7976", file2Data);
var dataFolder = GetBrukerDataFolder(dotDFolderName);
using (var reader = new MSDataFileReader(dataFolder.FullName))
{
Console.WriteLine("Scan data for {0}", dataFolder.Name);
Console.WriteLine("{0} {1,-8} {2,-8} {3,-8} {4,-8} {5,-8} {6}",
"Scan", "MzCount", "IntCount",
"FirstMz", "FirstInt", "MidMz", "MidInt");
var scanNumberToIndexMap = reader.GetScanToIndexMapping();
foreach (var scan in scanNumberToIndexMap.Where(x => x.Key >= scanStart && x.Key <= scanEnd))
{
var scanNumber = scan.Key;
var spectrumIndex = scan.Value;
var spectrum = reader.GetSpectrum(spectrumIndex, true);
var dataPointsRead = spectrum.Mzs.Length;
Assert.IsTrue(dataPointsRead > 0, "GetScanData returned 0 for scan {0}", scanNumber);
var midPoint = (int)(spectrum.Intensities.Length / 2f);
var scanSummary =
string.Format(
"{0} {1,-8} {2,-8} {3,-8:0.000} {4,-8:0.0E+0} {5,-8:0.000} {6:0.0E+0}",
scanNumber,
spectrum.Mzs.Length, spectrum.Intensities.Length,
spectrum.Mzs[0], spectrum.Intensities[0],
spectrum.Mzs[midPoint], spectrum.Intensities[midPoint]);
Console.WriteLine(scanSummary);
if (!expectedData.TryGetValue(Path.GetFileNameWithoutExtension(dataFolder.Name), out var expectedDataThisFile))
{
Assert.Fail("Dataset {0} not found in dictionary expectedData", dataFolder.Name);
}
if (expectedDataThisFile.TryGetValue(scanNumber, out var expectedDataDetails))
{
Assert.AreEqual(expectedDataDetails, scanSummary,
"Scan details mismatch, scan " + scanNumber);
}
}
}
}
public void TestCorruptDataHandling(
string dotDFolderName,
int scanStart,
int scanEnd,
int expectedMS1,
int expectedMS2)
{
var dataFolder = GetBrukerDataFolder(dotDFolderName);
try
{
using (var reader = new MSDataFileReader(dataFolder.FullName))
{
var scanCount = reader.SpectrumCount;
Console.WriteLine("Scan count for {0}: {1}", dataFolder.Name, scanCount);
if (expectedMS1 + expectedMS2 == 0)
{
Assert.IsTrue(scanCount == 0, "ScanCount is non-zero, while we expected it to be 0");
}
else
{
Assert.IsTrue(scanCount > 0, "ScanCount is zero, while we expected it to be > 0");
}
var scanNumberToIndexMap = reader.GetScanToIndexMapping();
var scanCountMS1 = 0;
var scanCountMS2 = 0;
foreach (var scan in scanNumberToIndexMap.Where(x => x.Key >= scanStart && x.Key <= scanEnd))
{
var scanNumber = scan.Key;
var spectrumIndex = scan.Value;
try
{
var spectrum = reader.GetSpectrum(spectrumIndex, true);
var cvScanInfo = reader.GetSpectrumScanInfo(spectrumIndex);
Assert.IsTrue(cvScanInfo != null, "GetSpectrumScanInfo returned a null object for scan {0}", scanNumber);
if (spectrum.Level > 1)
{
scanCountMS2++;
}
else
{
scanCountMS1++;
}
var dataPointCount = spectrum.Mzs.Length;
Assert.IsTrue(dataPointCount > 0, "Data point count is 0 for scan {0}", scanNumber);
Assert.IsTrue(spectrum.Mzs.Length > 0, "m/z data is empty for scan {0}", scanNumber);
Assert.IsTrue(spectrum.Intensities.Length > 0, "Intensity data is empty for scan {0}", scanNumber);
Assert.IsTrue(spectrum.Mzs.Length == spectrum.Intensities.Length, "Array length mismatch for m/z and intensity data for scan {0}", scanNumber);
}
catch (Exception ex)
{
Console.WriteLine("Exception reading scan {0}: {1}", scanNumber, ex.Message);
Assert.Fail("Exception reading scan {0}", scanNumber);
}
}
Console.WriteLine("scanCountMS1={0}", scanCountMS1);
Console.WriteLine("scanCountMS2={0}", scanCountMS2);
Assert.AreEqual(expectedMS1, scanCountMS1, "MS1 scan count mismatch");
Assert.AreEqual(expectedMS2, scanCountMS2, "MS2 scan count mismatch");
}
}
catch (Exception ex)
{
if (expectedMS1 + expectedMS2 == 0)
{
Console.WriteLine("Error opening .D folder (this was expected):\n{0}", ex.Message);
}
else
{
var msg = string.Format("Exception opening .D folder {0}:\n{1}", dotDFolderName, ex.Message);
Console.WriteLine(msg);
Assert.Fail(msg);
}
}
}
public void TestGetScanInfo(string dotDFolderName, int scanStart, int scanEnd, int expectedMS1, int expectedMS2)
{
var expectedData = new Dictionary <string, Dictionary <int, string> >();
// Keys in this dictionary are the scan number whose metadata is being retrieved
var file1Data = new Dictionary <int, string>
{
// Scan MSLevel NumPeaks RetentionTime ScanStartTime DriftTimeMsec LowMass HighMass TotalIonCurrent BasePeakMZ BasePeakIntensity ParentIonMZ
{ 1, "1 1 7794096 0.59 35.34 0 92 1300 7.1E+9 0.000 5.5E+8 0.00 positive False 696.00" },
{ 2, "2 1 7794096 1.10 66.27 0 92 1300 7.2E+9 0.000 5.6E+8 0.00 positive False 696.00" },
{ 3, "3 1 7794096 1.62 97.18 0 92 1300 7.2E+9 0.000 5.5E+8 0.00 positive False 696.00" },
{ 4, "4 1 7794096 2.14 128.17 0 92 1300 7.1E+9 0.000 5.3E+8 0.00 positive False 696.00" },
{ 5, "5 1 7794096 2.65 159.12 0 92 1300 7.1E+9 0.000 5.4E+8 0.00 positive False 696.00" }
};
expectedData.Add("2016_04_12_Background_000001", file1Data);
var file2Data = new Dictionary <int, string>
{
{ 1, "1 1 7615807 3.58 214.92 0 111 1200 3.6E+10 0.000 3.1E+9 0.00 negative False 655.50" }
};
expectedData.Add("Blank-2_05May16_Leopard_Infuse_1_01_7976", file2Data);
var file3Data = new Dictionary <int, string>
{
{ 15, "15 1 39775 2.38 142.89 0 983 984 0.0E+0 0.000 0.0E+0 0.00 positive False 983.50" },
{ 16, "16 1 39775 2.53 152.06 0 983 984 0.0E+0 0.000 0.0E+0 0.00 positive False 983.50" },
{ 17, "17 1 39775 2.69 161.24 0 983 984 0.0E+0 0.000 0.0E+0 0.00 positive False 983.50" },
{ 18, "18 1 39775 2.84 170.41 0 983 984 0.0E+0 0.000 0.0E+0 0.00 positive False 983.50" },
{ 19, "19 1 39775 2.99 179.58 0 983 984 0.0E+0 0.000 0.0E+0 0.00 positive False 983.50" },
{ 20, "20 1 39775 3.15 188.76 0 983 984 0.0E+0 0.000 0.0E+0 0.00 positive False 983.50" }
};
expectedData.Add("Humira_100fmol_20121026_hi_res_9_01_716", file3Data);
var file4Data = new Dictionary <int, string>
{
{ 1, "1 2 8214787 2.20 131.89 0 207 10000 6.0E+8 0.000 1.3E+7 1600.00 cid negative False 1600.00" }
};
expectedData.Add("MZ20160603PPS_edta_000004", file4Data);
var dataFolder = GetBrukerDataFolder(dotDFolderName);
using (var reader = new MSDataFileReader(dataFolder.FullName))
{
Console.WriteLine("Scan info for {0}", dataFolder.Name);
Console.WriteLine("{0} {1} {2} {3} {4} {5} {6} {7} {8} {9} {10} {11} {12} {13} {14} {15}",
"Scan", "MSLevel",
"NumPeaks", "RetentionTime",
"ScanStartTime",
"DriftTimeMsec",
"LowMass", "HighMass", "TotalIonCurrent",
"BasePeakMZ", "BasePeakIntensity",
"ParentIonMZ", "ActivationType",
"IonMode", "IsCentroided",
"IsolationMZ");
var scanNumberToIndexMap = reader.GetScanToIndexMapping();
var scanCountMS1 = 0;
var scanCountMS2 = 0;
foreach (var scan in scanNumberToIndexMap.Where(x => x.Key >= scanStart && x.Key <= scanEnd))
{
var scanNumber = scan.Key;
var spectrumIndex = scan.Value;
var spectrum = reader.GetSpectrum(spectrumIndex, true);
var spectrumParams = reader.GetSpectrumCVParamData(spectrumIndex);
var cvScanInfo = reader.GetSpectrumScanInfo(spectrumIndex);
Assert.IsTrue(spectrum != null, "GetSpectrum returned a null object for scan " + scanNumber);
var totalIonCurrent = cvParamUtilities.GetCvParamValueDbl(spectrumParams, cvParamUtilities.CVIDs.MS_TIC);
var basePeakMZ = cvParamUtilities.GetCvParamValueDbl(spectrumParams, cvParamUtilities.CVIDs.MS_base_peak_m_z);
var basePeakIntensity = cvParamUtilities.GetCvParamValueDbl(spectrumParams, cvParamUtilities.CVIDs.MS_base_peak_intensity);
double isolationMZ = 0;
double parentIonMZ = 0;
var activationType = string.Empty;
if (spectrum.Precursors.Length > 0)
{
var precursor = spectrum.Precursors[0];
isolationMZ = precursor.IsolationMz.GetValueOrDefault();
parentIonMZ = precursor.PrecursorMz.GetValueOrDefault();
if (precursor.ActivationTypes != null)
{
activationType = string.Join(", ", precursor.ActivationTypes);
}
}
GetScanMetadata(cvScanInfo, out var scanStartTime, out var lowMass, out var highMass);
var retentionTime = cvParamUtilities.CheckNull(spectrum.RetentionTime);
var numPeaks = spectrum.Mzs.Length;
var ionMode = spectrum.NegativeCharge ? "negative" : "positive";
var scanSummary =
string.Format(
"{0} {1} {2,5} {3,6:0.00} {4,6:0.00} {5:0} {6,3:0} {7,5:0} {8,6:0.0E+0} {9,8:0.000} {10,6:0.0E+0} {11,8:0.00} {12,-8} {13} {14,-5} {15,8:0.00}",
scanNumber, spectrum.Level,
numPeaks, retentionTime, scanStartTime,
cvParamUtilities.CheckNull(spectrum.DriftTimeMsec),
lowMass, highMass,
totalIonCurrent,
basePeakMZ, basePeakIntensity, parentIonMZ,
activationType,
ionMode, spectrum.Centroided, isolationMZ);
Console.WriteLine(scanSummary);
if (spectrum.Level > 1)
{
scanCountMS2++;
}
else
{
scanCountMS1++;
}
if (!expectedData.TryGetValue(Path.GetFileNameWithoutExtension(dataFolder.Name), out var expectedDataThisFile))
{
Assert.Fail("Dataset {0} not found in dictionary expectedData", dataFolder.Name);
}
if (expectedDataThisFile.TryGetValue(scanNumber, out var expectedScanSummary))
{
Assert.AreEqual(expectedScanSummary, scanSummary,
"Scan summary mismatch, scan " + scanNumber);
}
var expectedNativeId = string.Format("scan={0}", scanNumber);
Assert.AreEqual(spectrum.NativeId, expectedNativeId, "NativeId is not in the expected format for scan {0}", scanNumber);
}
Console.WriteLine("scanCountMS1={0}", scanCountMS1);
Console.WriteLine("scanCountMS2={0}", scanCountMS2);
Assert.AreEqual(expectedMS1, scanCountMS1, "MS1 scan count mismatch");
Assert.AreEqual(expectedMS2, scanCountMS2, "MS2 scan count mismatch");
}
}
public void TestGetScanData(string uimfFileName, int frameStart, int frameEnd)
{
var expectedData = new Dictionary <string, Dictionary <KeyValuePair <int, int>, string> >();
// Keys in this dictionary are the FrameNum, ScanNum whose metadata is being retrieved
var file1Data = new Dictionary <KeyValuePair <int, int>, string>
{
{ new KeyValuePair <int, int>(21, 1), " 21 1 171 171 73.143 0 4313.446 6" },
{ new KeyValuePair <int, int>(21, 45), " 21 45 132 132 49.420 0 2871.914 0" },
{ new KeyValuePair <int, int>(21, 90), " 21 90 58061 58061 33.139 0 892.171 0" },
{ new KeyValuePair <int, int>(21, 135), " 21 135 1332 1332 59.655 0 1455.314 0" },
{ new KeyValuePair <int, int>(21, 180), " 21 180 213 213 35.827 0 3477.878 16" },
{ new KeyValuePair <int, int>(21, 225), " 21 225 198 198 34.311 0 4724.490 0" },
{ new KeyValuePair <int, int>(21, 270), " 21 270 156 156 137.671 0 4960.353 0" },
{ new KeyValuePair <int, int>(22, 1), " 22 1 171 171 33.352 0 2700.500 2" },
{ new KeyValuePair <int, int>(22, 45), " 22 45 123 123 60.048 0 2958.660 2" },
{ new KeyValuePair <int, int>(22, 90), " 22 90 57811 57811 33.519 0 893.895 0" },
{ new KeyValuePair <int, int>(22, 135), " 22 135 1558 1558 33.800 0 1442.189 141" },
{ new KeyValuePair <int, int>(22, 180), " 22 180 165 165 104.876 0 2716.046 4" },
{ new KeyValuePair <int, int>(22, 225), " 22 225 165 165 49.372 0 5356.743 8" },
{ new KeyValuePair <int, int>(22, 270), " 22 270 168 168 41.214 0 3317.148 0" },
{ new KeyValuePair <int, int>(23, 1), " 23 1 159 159 44.206 0 2656.092 1" },
{ new KeyValuePair <int, int>(23, 45), " 23 45 179 179 66.354 0 4174.595 0" },
{ new KeyValuePair <int, int>(23, 90), " 23 90 59421 59421 33.319 0 901.566 17" },
{ new KeyValuePair <int, int>(23, 135), " 23 135 1398 1398 36.437 0 1429.296 0" },
{ new KeyValuePair <int, int>(23, 180), " 23 180 228 228 124.690 0 2244.101 0" },
{ new KeyValuePair <int, int>(23, 225), " 23 225 186 186 35.140 0 2326.136 0" },
{ new KeyValuePair <int, int>(23, 270), " 23 270 162 162 134.804 0 4518.062 0" }
};
expectedData.Add("9_Peptide_Mix_16Oct14_Cedar_Infuse", file1Data);
var file2Data = new Dictionary <KeyValuePair <int, int>, string>
{
{ new KeyValuePair <int, int>(50, 90), " 50 90 304 304 166.939 0 316.855 71" },
{ new KeyValuePair <int, int>(50, 135), " 50 135 36 36 479.959 0 532.950 0" },
{ new KeyValuePair <int, int>(51, 90), " 51 90 516 516 166.939 0 320.853 0" },
{ new KeyValuePair <int, int>(51, 135), " 51 135 27 27 474.824 0 532.934 38" },
{ new KeyValuePair <int, int>(51, 315), " 51 315 3 3 250.922 0 250.922 58" },
{ new KeyValuePair <int, int>(52, 90), " 52 90 579 579 166.939 0 319.857 61" },
{ new KeyValuePair <int, int>(52, 135), " 52 135 30 30 479.959 0 532.934 0" },
{ new KeyValuePair <int, int>(52, 315), " 52 315 3 3 250.922 0 250.922 67" },
{ new KeyValuePair <int, int>(53, 90), " 53 90 625 625 164.932 0 321.351 0" },
{ new KeyValuePair <int, int>(53, 135), " 53 135 39 39 391.282 0 532.934 47" },
{ new KeyValuePair <int, int>(54, 90), " 54 90 456 456 164.941 0 318.876 0" },
{ new KeyValuePair <int, int>(54, 135), " 54 135 33 33 391.282 0 530.978 17" },
{ new KeyValuePair <int, int>(55, 90), " 55 90 467 467 164.932 0 318.888 0" },
{ new KeyValuePair <int, int>(55, 135), " 55 135 24 24 479.959 0 532.950 0" }
};
expectedData.Add("QC_Shew_IMER_500ng_Run-1_4May16_Oak_15-01-16", file2Data);
var dataFile = GetUimfDataFile(uimfFileName);
using (var reader = new MSDataFileReader(dataFile.FullName))
{
Console.WriteLine("Scan data for {0}", dataFile.Name);
Console.WriteLine("{0,4} {1,4} {2,-8} {3,-8} {4,-8} {5,-8} {6,-8} {7}",
"Frame", "Scan", "MzCount", "IntCount",
"FirstMz", "FirstInt", "MidMz", "MidInt");
var frameScanPairToIndexMap = reader.GetUimfFrameScanPairToIndexMapping();
foreach (var frame in frameScanPairToIndexMap)
{
var frameNumber = frame.Key.Key;
var scanNumber = frame.Key.Value;
var spectrumIndex = frame.Value;
if (frameNumber < frameStart || frameNumber > frameEnd)
{
continue;
}
if (!(scanNumber == 1 || scanNumber % 45 == 0))
{
continue;
}
var spectrum = reader.GetSpectrum(spectrumIndex, true);
var dataPointsRead = spectrum.Mzs.Length;
if (dataPointsRead == 0)
{
Console.WriteLine("Frame {0}, scan {1} has no data; ignoring", frameNumber, scanNumber);
continue;
}
var midPoint = (int)(spectrum.Intensities.Length / 2f);
var scanSummary =
string.Format(
"{0,4} {1,4} {2,-8} {3,-8} {4,-8:0.000} {5,-8:0} {6,-8:0.000} {7:0}",
frameNumber, scanNumber,
spectrum.Mzs.Length, spectrum.Intensities.Length,
spectrum.Mzs[0], spectrum.Intensities[0],
spectrum.Mzs[midPoint], spectrum.Intensities[midPoint]);
Console.WriteLine(scanSummary);
if (!expectedData.TryGetValue(Path.GetFileNameWithoutExtension(dataFile.Name), out var expectedDataThisFile))
{
Assert.Fail("Dataset {0} not found in dictionary expectedData", dataFile.Name);
}
if (expectedDataThisFile.TryGetValue(new KeyValuePair <int, int>(frameNumber, scanNumber), out var expectedDataDetails))
{
Assert.AreEqual(expectedDataDetails, scanSummary,
"Scan details mismatch, scan " + scanNumber);
}
}
}
}
public void TestGetScanInfo(string uimfFileName, int frameStart, int frameEnd, int expectedMS1, int expectedMS2)
{
var expectedData = new Dictionary <string, Dictionary <KeyValuePair <int, int>, string> >();
// Keys in this dictionary are the FrameNum, ScanNum whose metadata is being retrieved
var file1Data = new Dictionary <KeyValuePair <int, int>, string>
{
// Scan MSLevel NumPeaks RetentionTime DriftTimeMsec IonMobilityDriftTime LowMass HighMass TotalIonCurrent BasePeakMZ BasePeakIntensity ParentIonMZ ActivationType IonMode IsCentroided ScanStartTime IonInjectionTime FilterText
{ new KeyValuePair <int, int>(1, 0), " 1 0 1 3 0.01 0.01 0.00 0.00 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(1, 100), " 1 100 1 1317 0.01 0.01 24.68 24.68 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(1, 200), " 1 200 1 3 0.01 0.01 49.36 49.36 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(2, 0), " 2 0 1 16 0.25 0.25 0.00 0.00 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(2, 1), " 2 1 1 6 0.25 0.25 0.25 0.25 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(2, 100), " 2 100 1 3429 0.25 0.25 24.70 24.70 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(2, 200), " 2 200 1 9 0.25 0.25 49.39 49.39 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(3, 0), " 3 0 1 21 0.50 0.50 0.00 0.00 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(3, 100), " 3 100 1 4216 0.50 0.50 24.65 24.65 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(3, 200), " 3 200 1 3 0.50 0.50 49.31 49.31 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(4, 0), " 4 0 1 3 0.75 0.75 0.00 0.00 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(4, 1), " 4 1 1 6 0.75 0.75 0.25 0.25 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(4, 100), " 4 100 1 5640 0.75 0.75 24.58 24.58 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(4, 200), " 4 200 1 6 0.75 0.75 49.16 49.16 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(5, 0), " 5 0 1 9 1.00 1.00 0.00 0.00 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(5, 100), " 5 100 1 4605 1.00 1.00 24.70 24.70 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" },
{ new KeyValuePair <int, int>(5, 200), " 5 200 1 3 1.00 1.00 49.39 49.39 0 14384 0.0E+0 0.000 0.0E+0 0.00 positive False 7192.23" }
};
expectedData.Add("9_Peptide_Mix_16Oct14_Cedar_Infuse", file1Data);
var file2Data = new Dictionary <KeyValuePair <int, int>, string>
{
{ new KeyValuePair <int, int>(1, 38), " 1 38 1 15 0.01 0.01 6.11 6.11 0 2646 0.0E+0 0.000 0.0E+0 0.00 positive False 1322.76" },
{ new KeyValuePair <int, int>(1, 114), " 1 114 1 1215 0.01 0.01 18.34 18.34 0 2646 0.0E+0 0.000 0.0E+0 0.00 positive False 1322.76" },
{ new KeyValuePair <int, int>(1, 152), " 1 152 1 222 0.01 0.01 24.45 24.45 0 2646 0.0E+0 0.000 0.0E+0 0.00 positive False 1322.76" },
{ new KeyValuePair <int, int>(1, 228), " 1 228 1 3 0.01 0.01 36.67 36.67 0 2646 0.0E+0 0.000 0.0E+0 0.00 positive False 1322.76" },
{ new KeyValuePair <int, int>(1, 304), " 1 304 1 9 0.01 0.01 48.89 48.89 0 2646 0.0E+0 0.000 0.0E+0 0.00 positive False 1322.76" }
};
expectedData.Add("9pep_mix_1uM_4bit_50_3Jun16", file2Data);
var file3Data = new Dictionary <KeyValuePair <int, int>, string>
{
{ new KeyValuePair <int, int>(1, 100), " 1 100 1 504 0.01 0.01 16.37 16.37 0 2646 0.0E+0 0.000 0.0E+0 0.00 positive False 1322.79" },
{ new KeyValuePair <int, int>(2, 100), " 2 100 1 494 0.06 0.06 16.42 16.42 0 2646 0.0E+0 0.000 0.0E+0 0.00 positive False 1322.79" },
{ new KeyValuePair <int, int>(3, 100), " 3 100 1 1109 0.11 0.11 16.43 16.43 0 2646 0.0E+0 0.000 0.0E+0 0.00 positive False 1322.79" },
{ new KeyValuePair <int, int>(4, 0), " 4 0 1 3 0.17 0.17 0.00 0.00 0 2646 0.0E+0 0.000 0.0E+0 0.00 positive False 1322.79" },
{ new KeyValuePair <int, int>(4, 100), " 4 100 1 1061 0.17 0.17 16.41 16.41 0 2646 0.0E+0 0.000 0.0E+0 0.00 positive False 1322.79" },
{ new KeyValuePair <int, int>(5, 0), " 5 0 1 3 0.22 0.22 0.00 0.00 0 2646 0.0E+0 0.000 0.0E+0 0.00 positive False 1322.79" },
{ new KeyValuePair <int, int>(5, 100), " 5 100 1 1087 0.22 0.22 16.44 16.44 0 2646 0.0E+0 0.000 0.0E+0 0.00 positive False 1322.79" },
};
expectedData.Add("QC_Shew_IMER_500ng_Run-1_4May16_Oak_15-01-16", file3Data);
var file4Data = new Dictionary <KeyValuePair <int, int>, string>
{
{ new KeyValuePair <int, int>(1, 1), " 1 1 1 344 0.00 0.00 0.12 0.12 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(1, 100), " 1 100 1 345 0.00 0.00 12.10 12.10 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(1, 200), " 1 200 1 577 0.00 0.00 24.20 24.20 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(1, 300), " 1 300 1 996 0.00 0.00 36.30 36.30 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(1, 400), " 1 400 1 469 0.00 0.00 48.40 48.40 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(1, 500), " 1 500 1 336 0.00 0.00 60.50 60.50 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(1, 600), " 1 600 1 369 0.00 0.00 72.60 72.60 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(1, 700), " 1 700 1 423 0.00 0.00 84.70 84.70 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(2, 1), " 2 1 1 381 0.00 0.00 0.12 0.12 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(2, 100), " 2 100 1 243 0.00 0.00 12.10 12.10 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(2, 200), " 2 200 1 669 0.00 0.00 24.20 24.20 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(2, 300), " 2 300 1 770 0.00 0.00 36.30 36.30 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(2, 400), " 2 400 1 372 0.00 0.00 48.40 48.40 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(2, 500), " 2 500 1 355 0.00 0.00 60.50 60.50 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(2, 600), " 2 600 1 441 0.00 0.00 72.60 72.60 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(2, 700), " 2 700 1 328 0.00 0.00 84.70 84.70 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(3, 1), " 3 1 1 405 0.00 0.00 0.12 0.12 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(3, 100), " 3 100 1 419 0.00 0.00 12.10 12.10 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(3, 200), " 3 200 1 705 0.00 0.00 24.20 24.20 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(3, 300), " 3 300 1 1080 0.00 0.00 36.30 36.30 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(3, 400), " 3 400 1 387 0.00 0.00 48.40 48.40 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(3, 500), " 3 500 1 423 0.00 0.00 60.50 60.50 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(3, 600), " 3 600 1 402 0.00 0.00 72.60 72.60 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(3, 700), " 3 700 1 333 0.00 0.00 84.70 84.70 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(4, 1), " 4 1 1 348 0.00 0.00 0.12 0.12 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(4, 100), " 4 100 1 343 0.00 0.00 12.10 12.10 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(4, 200), " 4 200 1 625 0.00 0.00 24.20 24.20 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(4, 300), " 4 300 1 1125 0.00 0.00 36.29 36.29 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(4, 400), " 4 400 1 384 0.00 0.00 48.39 48.39 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(4, 500), " 4 500 1 399 0.00 0.00 60.49 60.49 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(4, 600), " 4 600 1 362 0.00 0.00 72.59 72.59 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" },
{ new KeyValuePair <int, int>(4, 700), " 4 700 1 360 0.00 0.00 84.69 84.69 0 1700 0.0E+0 0.000 0.0E+0 0.00 positive False 849.87" }
};
expectedData.Add("20160524_TuneMix_1574V_neg_001", file4Data);
var dataFile = GetUimfDataFile(uimfFileName);
using (var reader = new MSDataFileReader(dataFile.FullName))
{
Console.WriteLine("Scan info for {0}", dataFile.Name);
Console.WriteLine("{0} {1} {2} {3} {4} {5} {6} {7} {8} {9} {10} {11} {12} {13} {14} {15} {16} {17}",
"Frame", "Scan", "MSLevel",
"NumPeaks", "RetentionTime",
"ScanStartTime",
"DriftTimeMsec",
"IonMobilityDriftTime",
"LowMass", "HighMass", "TotalIonCurrent",
"BasePeakMZ", "BasePeakIntensity",
"ParentIonMZ", "ActivationType",
"IonMode", "IsCentroided",
"IsolationMZ");
var frameScanPairToIndexMap = reader.GetUimfFrameScanPairToIndexMapping();
var scanCountMS1 = 0;
var scanCountMS2 = 0;
foreach (var frame in frameScanPairToIndexMap)
{
var frameNumber = frame.Key.Key;
var scanNumber = frame.Key.Value;
var spectrumIndex = frame.Value;
if (frameNumber < frameStart || frameNumber > frameEnd)
{
continue;
}
if (string.Equals(uimfFileName, "9pep_mix_1uM_4bit_50_3Jun16.uimf", StringComparison.InvariantCultureIgnoreCase))
{
if (!(scanNumber == 1 || scanNumber % 38 == 0))
{
continue;
}
}
else
{
if (!(scanNumber == 1 || scanNumber % 100 == 0))
{
continue;
}
}
var spectrum = reader.GetSpectrum(spectrumIndex, true);
var spectrumParams = reader.GetSpectrumCVParamData(spectrumIndex);
var cvScanInfo = reader.GetSpectrumScanInfo(spectrumIndex);
Assert.IsTrue(spectrum != null, "GetSpectrum returned a null object for frame {0}, scan {1} ", frameNumber, scanNumber);
var totalIonCurrent = cvParamUtilities.GetCvParamValueDbl(spectrumParams, cvParamUtilities.CVIDs.MS_TIC);
var basePeakMZ = cvParamUtilities.GetCvParamValueDbl(spectrumParams, cvParamUtilities.CVIDs.MS_base_peak_m_z);
var basePeakIntensity = cvParamUtilities.GetCvParamValueDbl(spectrumParams, cvParamUtilities.CVIDs.MS_base_peak_intensity);
double isolationMZ = 0;
double parentIonMZ = 0;
var activationType = string.Empty;
if (spectrum.Precursors.Length > 0)
{
var precursor = spectrum.Precursors[0];
isolationMZ = precursor.IsolationMz.GetValueOrDefault();
parentIonMZ = precursor.PrecursorMz.GetValueOrDefault();
if (precursor.ActivationTypes != null)
{
activationType = string.Join(", ", precursor.ActivationTypes);
}
}
GetScanMetadata(cvScanInfo, out var scanStartTime, out var ionMobilityDriftTime, out var lowMass, out var highMass);
var retentionTime = cvParamUtilities.CheckNull(spectrum.RetentionTime);
var numPeaks = spectrum.Mzs.Length;
var ionMode = spectrum.NegativeCharge ? "negative" : "positive";
var scanSummary =
string.Format(
"{0,4} {1,4} {2} {3,5} {4,6:0.00} {5,6:0.00} {6,8:0.00} {7,8:0.00} {8,3:0} {9,5:0} {10,6:0.0E+0} {11,8:0.000} {12,6:0.0E+0} {13,8:0.00} {14,-8} {15} {16,-5} {17,8:0.00}",
frameNumber, scanNumber, spectrum.Level,
numPeaks, retentionTime, scanStartTime,
cvParamUtilities.CheckNull(spectrum.DriftTimeMsec),
ionMobilityDriftTime,
lowMass, highMass,
totalIonCurrent, basePeakMZ, basePeakIntensity, parentIonMZ,
activationType, ionMode,
spectrum.Centroided, isolationMZ);
Console.WriteLine(scanSummary);
if (spectrum.Level > 1)
{
scanCountMS2++;
}
else
{
scanCountMS1++;
}
if (!expectedData.TryGetValue(Path.GetFileNameWithoutExtension(dataFile.Name), out var expectedDataThisFile))
{
Assert.Fail("Dataset {0} not found in dictionary expectedData", dataFile.Name);
}
if (expectedDataThisFile.TryGetValue(new KeyValuePair <int, int>(frameNumber, scanNumber), out var expectedScanSummary))
{
if (!string.Equals(expectedScanSummary, scanSummary))
{
Console.WriteLine(
"{0,4} {1,4} {2} {3,5} {4,6} {5,6} {6,8} {7,8} {8,3} {9,5} {10,6} {11,8} {12,6} {13,8} {14,-8} {15} {16,-5} {17,8}",
"Frame", "Scan", "MSLevel",
"NumPeaks", "RetentionTime", "ScanStartTime",
"DriftTimeMsec",
"IonMobilityDriftTime",
"LowMass", "HighMass",
"TIC", "BasePeakMZ", "BPI", "ParentIonMZ",
"ActivationType", "IonMode",
"Centroided?", "IsolationMZ");
}
Assert.AreEqual(expectedScanSummary, scanSummary,
"Scan summary mismatch, scan " + scanNumber);
}
var expectedNativeId = string.Format("frame={0} scan={1} frameType=1", frameNumber, scanNumber);
Assert.AreEqual(spectrum.NativeId, expectedNativeId, "NativeId is not in the expected format for frame {0}, scan {1} ", frameNumber, scanNumber);
}
Console.WriteLine("scanCountMS1={0}", scanCountMS1);
Console.WriteLine("scanCountMS2={0}", scanCountMS2);
Assert.AreEqual(expectedMS1, scanCountMS1, "MS1 scan count mismatch");
Assert.AreEqual(expectedMS2, scanCountMS2, "MS2 scan count mismatch");
}
}
public void TestCorruptDataHandling(
string uimfFileName,
int frameStart,
int frameEnd,
int expectedMS1,
int expectedMS2,
int expectedScansWithData)
{
var dataFile = GetUimfDataFile(uimfFileName);
try
{
using (var reader = new MSDataFileReader(dataFile.FullName))
{
var scanCount = reader.SpectrumCount;
Console.WriteLine("Scan count for {0}: {1}", dataFile.Name, scanCount);
if (expectedMS1 + expectedMS2 == 0)
{
Assert.IsTrue(scanCount == 0, "ScanCount is non-zero, while we expected it to be 0");
}
else
{
Assert.IsTrue(scanCount > 0, "ScanCount is zero, while we expected it to be > 0");
}
var frameScanPairToIndexMap = reader.GetUimfFrameScanPairToIndexMapping();
var scanCountMS1 = 0;
var scanCountMS2 = 0;
var scansWithData = 0;
foreach (var frame in frameScanPairToIndexMap)
{
var frameNumber = frame.Key.Key;
var scanNumber = frame.Key.Value;
var spectrumIndex = frame.Value;
if (frameNumber < frameStart || frameNumber > frameEnd)
{
continue;
}
try
{
var spectrum = reader.GetSpectrum(spectrumIndex, true);
var cvScanInfo = reader.GetSpectrumScanInfo(spectrumIndex);
Assert.IsTrue(cvScanInfo != null, "GetSpectrumScanInfo returned a null object for frame {0}, scan {1} ", frameNumber, scanNumber);
if (spectrum.Level > 1)
{
scanCountMS2++;
}
else
{
scanCountMS1++;
}
var dataPointCount = spectrum.Mzs.Length;
if (dataPointCount > 0)
{
scansWithData++;
}
Assert.IsTrue(spectrum.Mzs.Length == spectrum.Intensities.Length, "Array length mismatch for m/z and intensity data for frame {0}, scan {1} ", frameNumber, scanNumber);
}
catch (Exception ex)
{
Console.WriteLine("Exception reading scan {0}: {1}", scanNumber, ex.Message);
Assert.Fail("Exception reading scan {0}", scanNumber);
}
}
Console.WriteLine("scanCountMS1={0}", scanCountMS1);
Console.WriteLine("scanCountMS2={0}", scanCountMS2);
Console.WriteLine("scansWithData={0}", scansWithData);
Assert.AreEqual(expectedMS1, scanCountMS1, "MS1 scan count mismatch");
Assert.AreEqual(expectedMS2, scanCountMS2, "MS2 scan count mismatch");
Assert.AreEqual(expectedScansWithData, scansWithData, "ScansWithData count mismatch");
}
}
catch (Exception ex)
{
if (expectedMS1 + expectedMS2 == 0)
{
Console.WriteLine("Error opening .uimf file (this was expected):\n{0}", ex.Message);
}
else
{
var msg = string.Format("Exception opening .uimf file {0}:\n{1}", uimfFileName, ex.Message);
Console.WriteLine(msg);
Assert.Fail(msg);
}
}
}
