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clsMRMProcessing.cs
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clsMRMProcessing.cs
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using System;
using System.Collections.Generic;
using System.IO;
using MASIC.DataOutput;
using MASIC.Options;
using MASICPeakFinder;
using PRISM;
using ThermoRawFileReader;
namespace MASIC
{
/// <summary>
/// MRM processing class
/// </summary>
public class clsMRMProcessing : clsMasicEventNotifier
{
// Ignore Spelling: crosstab, mrm, srm
private struct SRMListType
{
public double ParentIonMZ;
public double CentralMass;
public override string ToString()
{
return "m/z " + ParentIonMZ.ToString("0.00");
}
}
private readonly MASICOptions mOptions;
private readonly clsDataAggregation mDataAggregation;
private readonly clsDataOutput mDataOutputHandler;
/// <summary>
/// Constructor
/// </summary>
public clsMRMProcessing(MASICOptions masicOptions, clsDataOutput dataOutputHandler)
{
mOptions = masicOptions;
mDataAggregation = new clsDataAggregation();
RegisterEvents(mDataAggregation);
mDataOutputHandler = dataOutputHandler;
}
private string ConstructSRMMapKey(SRMListType srmEntry)
{
return ConstructSRMMapKey(srmEntry.ParentIonMZ, srmEntry.CentralMass);
}
private string ConstructSRMMapKey(double parentIonMZ, double centralMass)
{
return parentIonMZ.ToString("0.000") + "_to_" + centralMass.ToString("0.000");
}
private bool DetermineMRMSettings(
clsScanList scanList,
out List<clsMRMScanInfo> mrmSettings,
out List<SRMListType> srmList)
{
// Returns true if this dataset has MRM data and if it is parsed successfully
// Returns false if the dataset does not have MRM data, or if an error occurs
mrmSettings = new List<clsMRMScanInfo>(200);
srmList = new List<SRMListType>(600); // Assume there are 3 fragmentation masses for each parent mass
try
{
var mrmDataPresent = false;
UpdateProgress(0, "Determining MRM settings");
// Initialize the tracking arrays
var mrmHashToIndexMap = new Dictionary<string, clsMRMScanInfo>();
// Construct a list of the MRM search values used
foreach (var fragScan in scanList.FragScans)
{
if (fragScan.MRMScanType == MRMScanTypeConstants.SRM)
{
mrmDataPresent = true;
// See if this MRM spec is already in mrmSettings
var mrmInfoHash = GenerateMRMInfoHash(fragScan.MRMScanInfo);
if (!mrmHashToIndexMap.TryGetValue(mrmInfoHash, out var mrmInfoForHash))
{
mrmInfoForHash = DuplicateMRMInfo(fragScan.MRMScanInfo);
mrmInfoForHash.ScanCount = 1;
mrmInfoForHash.ParentIonInfoIndex = fragScan.FragScanInfo.ParentIonInfoIndex;
mrmSettings.Add(mrmInfoForHash);
mrmHashToIndexMap.Add(mrmInfoHash, mrmInfoForHash);
// Append the new entries to srmList
for (var mrmMassIndex = 0; mrmMassIndex < mrmInfoForHash.MRMMassCount; mrmMassIndex++)
{
// Add this new transition to srmList() only if not already present
var matchFound = false;
foreach (var srmItem in srmList)
{
if (MRMParentDaughterMatch(srmItem, mrmInfoForHash, mrmMassIndex))
{
matchFound = true;
break;
}
}
if (!matchFound)
{
// Entry is not yet present; add it
var newSRMItem = new SRMListType
{
ParentIonMZ = mrmInfoForHash.ParentIonMZ,
CentralMass = mrmInfoForHash.MRMMassList[mrmMassIndex].CentralMass
};
srmList.Add(newSRMItem);
}
}
}
else
{
mrmInfoForHash.ScanCount++;
}
}
}
// Resize the lists to their contents
mrmSettings.Capacity = mrmSettings.Count;
srmList.Capacity = srmList.Count;
return mrmDataPresent;
}
catch (Exception ex)
{
ReportError("Error determining the MRM settings", ex, clsMASIC.MasicErrorCodes.OutputFileWriteError);
return false;
}
}
/// <summary>
/// Duplicate MRM info, overriding the parent ion m/z using parentIonMZ
/// </summary>
/// <param name="sourceInfo"></param>
/// <param name="parentIonMZ"></param>
public static clsMRMScanInfo DuplicateMRMInfo(
MRMInfo sourceInfo,
double parentIonMZ)
{
var targetInfo = new clsMRMScanInfo
{
ParentIonMZ = parentIonMZ,
MRMMassCount = sourceInfo.MRMMassList.Count,
ScanCount = 0,
ParentIonInfoIndex = -1,
};
if (sourceInfo.MRMMassList == null)
{
targetInfo.MRMMassList = new List<MRMMassRangeType>();
}
else
{
targetInfo.MRMMassList = new List<MRMMassRangeType>(sourceInfo.MRMMassList.Count);
targetInfo.MRMMassList.AddRange(sourceInfo.MRMMassList);
}
return targetInfo;
}
/// <summary>
/// Duplicate MRM info
/// </summary>
/// <param name="sourceInfo"></param>
private clsMRMScanInfo DuplicateMRMInfo(clsMRMScanInfo sourceInfo)
{
var targetInfo = new clsMRMScanInfo
{
ParentIonMZ = sourceInfo.ParentIonMZ,
MRMMassCount = sourceInfo.MRMMassCount,
ScanCount = sourceInfo.ScanCount,
ParentIonInfoIndex = sourceInfo.ParentIonInfoIndex,
};
if (sourceInfo.MRMMassList == null)
{
targetInfo.MRMMassList = new List<MRMMassRangeType>();
}
else
{
targetInfo.MRMMassList = new List<MRMMassRangeType>(sourceInfo.MRMMassList.Count);
targetInfo.MRMMassList.AddRange(sourceInfo.MRMMassList);
}
return targetInfo;
}
/// <summary>
/// Export MRM data to disk
/// </summary>
/// <param name="scanList"></param>
/// <param name="spectraCache"></param>
/// <param name="inputFileName"></param>
/// <param name="outputDirectoryPath"></param>
public bool ExportMRMDataToDisk(
clsScanList scanList,
clsSpectraCache spectraCache,
string inputFileName,
string outputDirectoryPath)
{
if (!DetermineMRMSettings(scanList, out var mrmSettings, out var srmList))
{
return false;
}
return ExportMRMDataToDisk(scanList, spectraCache, mrmSettings, srmList, inputFileName, outputDirectoryPath);
}
/// <summary>
/// Export MRM data to disk
/// </summary>
/// <param name="scanList"></param>
/// <param name="spectraCache"></param>
/// <param name="mrmSettings"></param>
/// <param name="srmList"></param>
/// <param name="inputFileName"></param>
/// <param name="outputDirectoryPath"></param>
/// <returns>True if the MRM data is successfully written to disk, or if the mrmSettings list is empty</returns>
private bool ExportMRMDataToDisk(
clsScanList scanList,
clsSpectraCache spectraCache,
IReadOnlyList<clsMRMScanInfo> mrmSettings,
IReadOnlyList<SRMListType> srmList,
string inputFileName,
string outputDirectoryPath)
{
const char TAB_DELIMITER = '\t';
StreamWriter dataWriter = null;
StreamWriter crosstabWriter = null;
bool success;
try
{
// Only write this data if 1 or more fragmentation spectra are of type SRM
if (mrmSettings == null || mrmSettings.Count == 0)
{
return true;
}
UpdateProgress(0, "Exporting MRM data");
// Write out the MRM Settings
var mrmSettingsFilePath = clsDataOutput.ConstructOutputFilePath(
inputFileName, outputDirectoryPath, clsDataOutput.OutputFileTypeConstants.MRMSettingsFile);
using var settingsWriter = new StreamWriter(mrmSettingsFilePath);
settingsWriter.WriteLine(mDataOutputHandler.GetHeadersForOutputFile(scanList, clsDataOutput.OutputFileTypeConstants.MRMSettingsFile));
var dataColumns = new List<string>(7);
for (var mrmInfoIndex = 0; mrmInfoIndex < mrmSettings.Count; mrmInfoIndex++)
{
var mrmSetting = mrmSettings[mrmInfoIndex];
for (var mrmMassIndex = 0; mrmMassIndex < mrmSetting.MRMMassCount; mrmMassIndex++)
{
dataColumns.Clear();
dataColumns.Add(mrmInfoIndex.ToString());
dataColumns.Add(mrmSetting.ParentIonMZ.ToString("0.000"));
dataColumns.Add(mrmSetting.MRMMassList[mrmMassIndex].CentralMass.ToString("0.000"));
dataColumns.Add(mrmSetting.MRMMassList[mrmMassIndex].StartMass.ToString("0.000"));
dataColumns.Add(mrmSetting.MRMMassList[mrmMassIndex].EndMass.ToString("0.000"));
dataColumns.Add(mrmSetting.ScanCount.ToString());
settingsWriter.WriteLine(string.Join(TAB_DELIMITER.ToString(), dataColumns));
}
}
if (mOptions.WriteMRMDataList || mOptions.WriteMRMIntensityCrosstab)
{
// Populate srmKeyToIndexMap
var srmKeyToIndexMap = new Dictionary<string, int>();
for (var srmIndex = 0; srmIndex < srmList.Count; srmIndex++)
{
srmKeyToIndexMap.Add(ConstructSRMMapKey(srmList[srmIndex]), srmIndex);
}
if (mOptions.WriteMRMDataList)
{
// Write out the raw MRM Data
var dataFilePath = clsDataOutput.ConstructOutputFilePath(inputFileName, outputDirectoryPath, clsDataOutput.OutputFileTypeConstants.MRMDatafile);
dataWriter = new StreamWriter(dataFilePath);
// Write the file headers
dataWriter.WriteLine(mDataOutputHandler.GetHeadersForOutputFile(scanList, clsDataOutput.OutputFileTypeConstants.MRMDatafile));
}
if (mOptions.WriteMRMIntensityCrosstab)
{
// Write out the raw MRM Data
var crosstabFilePath = clsDataOutput.ConstructOutputFilePath(inputFileName, outputDirectoryPath, clsDataOutput.OutputFileTypeConstants.MRMCrosstabFile);
crosstabWriter = new StreamWriter(crosstabFilePath);
// Initialize the crosstab header variable using the data in srmList()
var headerNames = new List<string>(srmList.Count + 2)
{
"Scan_First",
"ScanTime"
};
foreach (var srmEntry in srmList)
{
headerNames.Add(ConstructSRMMapKey(srmEntry));
}
crosstabWriter.WriteLine(string.Join(TAB_DELIMITER.ToString(), headerNames));
}
var scanFirst = int.MinValue;
float scanTimeFirst = 0;
var srmIndexLast = 0;
var crosstabColumnValue = new double[srmList.Count];
var crosstabColumnFlag = new bool[srmList.Count];
// For scanIndex = 0 To scanList.FragScanCount - 1
foreach (var fragScan in scanList.FragScans)
{
if (fragScan.MRMScanType != MRMScanTypeConstants.SRM)
{
continue;
}
if (scanFirst == int.MinValue)
{
scanFirst = fragScan.ScanNumber;
scanTimeFirst = fragScan.ScanTime;
}
// Look for each of the m/z values specified in fragScan.MRMScanInfo.MRMMassList
for (var mrmMassIndex = 0; mrmMassIndex < fragScan.MRMScanInfo.MRMMassCount; mrmMassIndex++)
{
// Find the maximum value between fragScan.StartMass and fragScan.EndMass
// Need to define a tolerance to account for numeric rounding artifacts in the variables
var mzStart = fragScan.MRMScanInfo.MRMMassList[mrmMassIndex].StartMass;
var mzEnd = fragScan.MRMScanInfo.MRMMassList[mrmMassIndex].EndMass;
var mrmToleranceHalfWidth = Math.Round((mzEnd - mzStart) / 2, 6);
if (mrmToleranceHalfWidth < 0.001)
{
mrmToleranceHalfWidth = 0.001;
}
var matchFound = mDataAggregation.FindMaxValueInMZRange(
spectraCache, fragScan,
mzStart - mrmToleranceHalfWidth,
mzEnd + mrmToleranceHalfWidth,
out _, out var matchIntensity);
if (mOptions.WriteMRMDataList)
{
dataColumns.Clear();
dataColumns.Add(fragScan.ScanNumber.ToString());
dataColumns.Add(fragScan.MRMScanInfo.ParentIonMZ.ToString("0.000"));
if (matchFound)
{
dataColumns.Add(fragScan.MRMScanInfo.MRMMassList[mrmMassIndex].CentralMass.ToString("0.000"));
dataColumns.Add(matchIntensity.ToString("0.000"));
}
else
{
dataColumns.Add(fragScan.MRMScanInfo.MRMMassList[mrmMassIndex].CentralMass.ToString("0.000"));
dataColumns.Add("0");
}
dataWriter?.WriteLine(string.Join(TAB_DELIMITER.ToString(), dataColumns));
}
if (!mOptions.WriteMRMIntensityCrosstab)
continue;
var srmMapKey = ConstructSRMMapKey(fragScan.MRMScanInfo.ParentIonMZ, fragScan.MRMScanInfo.MRMMassList[mrmMassIndex].CentralMass);
// Use srmKeyToIndexMap to determine the appropriate column index for srmMapKey
if (srmKeyToIndexMap.TryGetValue(srmMapKey, out var srmIndex))
{
if (crosstabColumnFlag[srmIndex] ||
srmIndex == 0 && srmIndexLast == srmList.Count - 1)
{
// Either the column is already populated, or the SRMIndex has cycled back to zero
// Write out the current crosstab line and reset the crosstab column arrays
ExportMRMDataWriteLine(crosstabWriter, scanFirst, scanTimeFirst,
crosstabColumnValue,
crosstabColumnFlag,
TAB_DELIMITER, true);
scanFirst = fragScan.ScanNumber;
scanTimeFirst = fragScan.ScanTime;
}
if (matchFound)
{
crosstabColumnValue[srmIndex] = matchIntensity;
}
crosstabColumnFlag[srmIndex] = true;
srmIndexLast = srmIndex;
}
else
{
// Unknown combination of parent ion m/z and daughter m/z; this is unexpected
// We won't write this entry out
}
}
UpdateCacheStats(spectraCache);
if (mOptions.AbortProcessing)
{
break;
}
}
if (mOptions.WriteMRMIntensityCrosstab)
{
// Write out any remaining crosstab values
ExportMRMDataWriteLine(crosstabWriter, scanFirst, scanTimeFirst, crosstabColumnValue, crosstabColumnFlag, TAB_DELIMITER, false);
}
}
success = true;
}
catch (Exception ex)
{
ReportError("Error writing the SRM data to disk", ex, clsMASIC.MasicErrorCodes.OutputFileWriteError);
success = false;
}
finally
{
dataWriter?.Close();
crosstabWriter?.Close();
}
return success;
}
/// <summary>
/// Write one line to the export file
/// </summary>
/// <param name="writer"></param>
/// <param name="scanFirst"></param>
/// <param name="scanTimeFirst"></param>
/// <param name="crosstabColumnValue"></param>
/// <param name="crosstabColumnFlag"></param>
/// <param name="delimiter"></param>
/// <param name="forceWrite">If false, only write out the line if 1 or more columns is non-zero</param>
private void ExportMRMDataWriteLine(
TextWriter writer,
int scanFirst,
float scanTimeFirst,
IList<double> crosstabColumnValue,
IList<bool> crosstabColumnFlag,
char delimiter,
bool forceWrite)
{
var nonZeroCount = 0;
var dataColumns = new List<string>(crosstabColumnValue.Count + 2)
{
scanFirst.ToString(),
StringUtilities.DblToString(scanTimeFirst, 5)
};
// Construct a tab-delimited list of the values
// At the same time, clear the arrays
for (var index = 0; index < crosstabColumnValue.Count; index++)
{
if (crosstabColumnValue[index] > 0)
{
dataColumns.Add(crosstabColumnValue[index].ToString("0.000"));
nonZeroCount++;
}
else
{
dataColumns.Add("0");
}
crosstabColumnValue[index] = 0;
crosstabColumnFlag[index] = false;
}
if (nonZeroCount > 0 || forceWrite)
{
writer.WriteLine(string.Join(delimiter.ToString(), dataColumns));
}
}
private string GenerateMRMInfoHash(clsMRMScanInfo mrmScanInfo)
{
var hashValue = mrmScanInfo.ParentIonMZ + "_" + mrmScanInfo.MRMMassCount;
for (var index = 0; index < mrmScanInfo.MRMMassCount; index++)
{
hashValue += "_" +
mrmScanInfo.MRMMassList[index].CentralMass.ToString("0.000") + "_" +
mrmScanInfo.MRMMassList[index].StartMass.ToString("0.000") + "_" +
mrmScanInfo.MRMMassList[index].EndMass.ToString("0.000");
}
return hashValue;
}
private bool MRMParentDaughterMatch(
SRMListType udtSRMListEntry,
clsMRMScanInfo mrmSettingsEntry,
int mrmMassIndex)
{
return MRMParentDaughterMatch(
udtSRMListEntry.ParentIonMZ,
udtSRMListEntry.CentralMass,
mrmSettingsEntry.ParentIonMZ,
mrmSettingsEntry.MRMMassList[mrmMassIndex].CentralMass);
}
private bool MRMParentDaughterMatch(
double parentIonMZ1,
double mrmDaughterMZ1,
double parentIonMZ2,
double mrmDaughterMZ2)
{
const double COMPARISON_TOLERANCE = 0.01;
return Math.Abs(parentIonMZ1 - parentIonMZ2) <= COMPARISON_TOLERANCE &&
Math.Abs(mrmDaughterMZ1 - mrmDaughterMZ2) <= COMPARISON_TOLERANCE;
}
/// <summary>
/// Process MRM data
/// </summary>
/// <param name="scanList"></param>
/// <param name="spectraCache"></param>
/// <param name="sicProcessor"></param>
/// <param name="xmlResultsWriter"></param>
/// <param name="peakFinder"></param>
/// <param name="parentIonsProcessed"></param>
public bool ProcessMRMList(
clsScanList scanList,
clsSpectraCache spectraCache,
clsSICProcessing sicProcessor,
clsXMLResultsWriter xmlResultsWriter,
clsMASICPeakFinder peakFinder,
ref int parentIonsProcessed)
{
try
{
// Initialize sicDetails
var sicDetails = new clsSICDetails();
sicDetails.Reset();
sicDetails.SICScanType = clsScanList.ScanTypeConstants.FragScan;
for (var parentIonIndex = 0; parentIonIndex < scanList.ParentIons.Count; parentIonIndex++)
{
if (scanList.ParentIons[parentIonIndex].MRMDaughterMZ <= 0)
{
continue;
}
// Step 1: Create the SIC for this MRM Parent/Daughter pair
var parentIonMZ = scanList.ParentIons[parentIonIndex].MZ;
var mrmDaughterMZ = scanList.ParentIons[parentIonIndex].MRMDaughterMZ;
var searchToleranceHalfWidth = scanList.ParentIons[parentIonIndex].MRMToleranceHalfWidth;
// Reset SICData
sicDetails.SICData.Clear();
// Step through the fragmentation spectra, finding those that have matching parent and daughter ion m/z values
for (var scanIndex = 0; scanIndex < scanList.FragScans.Count; scanIndex++)
{
if (scanList.FragScans[scanIndex].MRMScanType != MRMScanTypeConstants.SRM)
{
continue;
}
var fragScan = scanList.FragScans[scanIndex];
var useScan = false;
for (var mrmMassIndex = 0; mrmMassIndex < fragScan.MRMScanInfo.MRMMassCount; mrmMassIndex++)
{
if (MRMParentDaughterMatch(fragScan.MRMScanInfo.ParentIonMZ,
fragScan.MRMScanInfo.MRMMassList[mrmMassIndex].CentralMass,
parentIonMZ, mrmDaughterMZ))
{
useScan = true;
break;
}
}
if (!useScan)
continue;
// Include this scan in the SIC for this parent ion
mDataAggregation.FindMaxValueInMZRange(spectraCache,
scanList.FragScans[scanIndex],
mrmDaughterMZ - searchToleranceHalfWidth,
mrmDaughterMZ + searchToleranceHalfWidth,
out var closestMZ, out var matchIntensity);
sicDetails.AddData(fragScan.ScanNumber, matchIntensity, closestMZ, scanIndex);
}
// Step 2: Find the largest peak in the SIC
// Compute the noise level; the noise level may change with increasing index number if the background is increasing for a given m/z
var success = peakFinder.ComputeDualTrimmedNoiseLevelTTest(sicDetails.SICIntensities, 0,
sicDetails.SICDataCount - 1,
mOptions.SICOptions.SICPeakFinderOptions.
SICBaselineNoiseOptions,
out var noiseStatsSegments);
if (!success)
{
SetLocalErrorCode(clsMASIC.MasicErrorCodes.FindSICPeaksError, true);
return false;
}
// Initialize the peak
scanList.ParentIons[parentIonIndex].SICStats.Peak = new clsSICStatsPeak();
// Find the data point with the maximum intensity
double maximumIntensity = 0;
scanList.ParentIons[parentIonIndex].SICStats.Peak.IndexObserved = 0;
for (var scanIndex = 0; scanIndex < sicDetails.SICDataCount; scanIndex++)
{
var intensity = sicDetails.SICIntensities[scanIndex];
if (intensity > maximumIntensity)
{
maximumIntensity = intensity;
scanList.ParentIons[parentIonIndex].SICStats.Peak.IndexObserved = scanIndex;
}
}
// Compute the minimum potential peak area in the entire SIC, populating potentialAreaStatsInFullSIC
peakFinder.FindPotentialPeakArea(sicDetails.SICData,
out var potentialAreaStatsInFullSIC,
mOptions.SICOptions.SICPeakFinderOptions);
// Update .BaselineNoiseStats in scanList.ParentIons(parentIonIndex).SICStats.Peak
scanList.ParentIons[parentIonIndex].SICStats.Peak.BaselineNoiseStats = peakFinder.LookupNoiseStatsUsingSegments(
scanList.ParentIons[parentIonIndex].SICStats.Peak.IndexObserved,
noiseStatsSegments);
var parentIon = scanList.ParentIons[parentIonIndex];
// Clear potentialAreaStatsForPeak
parentIon.SICStats.SICPotentialAreaStatsForPeak = new clsSICPotentialAreaStats();
var peakIsValid = peakFinder.FindSICPeakAndArea(sicDetails.SICData,
out var potentialAreaStatsForPeakOut,
parentIon.SICStats.Peak, out var smoothedYDataSubset,
mOptions.SICOptions.SICPeakFinderOptions,
potentialAreaStatsInFullSIC, false,
scanList.SIMDataPresent, false);
parentIon.SICStats.SICPotentialAreaStatsForPeak = potentialAreaStatsForPeakOut;
sicProcessor.StorePeakInParentIon(scanList, parentIonIndex, sicDetails,
parentIon.SICStats.SICPotentialAreaStatsForPeak,
parentIon.SICStats.Peak, peakIsValid);
// Step 3: store the results
// Possibly save the stats for this SIC to the SICData file
mDataOutputHandler.SaveSICDataToText(mOptions.SICOptions, scanList, parentIonIndex, sicDetails);
// Save the stats for this SIC to the XML file
xmlResultsWriter.SaveDataToXML(scanList, parentIonIndex, sicDetails, smoothedYDataSubset,
mDataOutputHandler);
parentIonsProcessed++;
// ---------------------------------------------------------
// Update progress
// ---------------------------------------------------------
try
{
if (scanList.ParentIons.Count > 1)
{
UpdateProgress((short)(parentIonsProcessed / (double)(scanList.ParentIons.Count - 1) * 100));
}
else
{
UpdateProgress(0);
}
UpdateCacheStats(spectraCache);
if (mOptions.AbortProcessing)
{
scanList.ProcessingIncomplete = true;
break;
}
if (parentIonsProcessed % 100 == 0)
{
if (DateTime.UtcNow.Subtract(mOptions.LastParentIonProcessingLogTime).TotalSeconds >= 10 || parentIonsProcessed % 500 == 0)
{
ReportMessage("Parent Ions Processed: " + parentIonsProcessed);
Console.Write(".");
mOptions.LastParentIonProcessingLogTime = DateTime.UtcNow;
}
}
}
catch (Exception ex)
{
ReportError("Error updating progress", ex, clsMASIC.MasicErrorCodes.CreateSICsError);
}
}
return true;
}
catch (Exception ex)
{
ReportError("Error creating SICs for MRM spectra", ex, clsMASIC.MasicErrorCodes.CreateSICsError);
return false;
}
}
}
}