/// <summary>
/// Store custom SIC values defined in CustomMZSearchValues
/// </summary>
/// <param name="scanList"></param>
/// <param name="defaultSICTolerance"></param>
/// <param name="sicToleranceIsPPM"></param>
/// <param name="defaultScanOrAcqTimeTolerance"></param>
public void AddCustomSICValues(
clsScanList scanList,
double defaultSICTolerance,
bool sicToleranceIsPPM,
float defaultScanOrAcqTimeTolerance)
{
var scanOrAcqTimeSumCount = 0;
float scanOrAcqTimeSumForAveraging = 0;
try
{
if (CustomMZSearchValues.Count == 0)
{
return;
}
var scanNumScanConverter = new clsScanNumScanTimeConversion();
RegisterEvents(scanNumScanConverter);
foreach (var customMzSearchValue in CustomMZSearchValues)
{
// Add a new parent ion entry to .ParentIons() for this custom MZ value
var currentParentIon = new clsParentIonInfo(customMzSearchValue.MZ);
if (customMzSearchValue.ScanOrAcqTimeCenter < float.Epsilon)
{
// Set the SurveyScanIndex to the center of the analysis
currentParentIon.SurveyScanIndex = scanNumScanConverter.FindNearestSurveyScanIndex(
scanList, 0.5F, eCustomSICScanTypeConstants.Relative);
}
else
{
currentParentIon.SurveyScanIndex = scanNumScanConverter.FindNearestSurveyScanIndex(
scanList, customMzSearchValue.ScanOrAcqTimeCenter, ScanToleranceType);
}
// Find the next MS2 scan that occurs after the survey scan (parent scan)
var surveyScanNumberAbsolute = 0;
if (currentParentIon.SurveyScanIndex < scanList.SurveyScans.Count)
{
surveyScanNumberAbsolute = scanList.SurveyScans[currentParentIon.SurveyScanIndex].ScanNumber + 1;
}
if (scanList.MasterScanOrderCount == 0)
{
currentParentIon.FragScanIndices.Add(0);
}
else
{
var fragScanIndexMatch = clsBinarySearch.BinarySearchFindNearest(
scanList.MasterScanNumList,
surveyScanNumberAbsolute,
clsBinarySearch.eMissingDataModeConstants.ReturnClosestPoint);
while (fragScanIndexMatch < scanList.MasterScanOrderCount && scanList.MasterScanOrder[fragScanIndexMatch].ScanType == clsScanList.eScanTypeConstants.SurveyScan)
{
fragScanIndexMatch += 1;
}
if (fragScanIndexMatch == scanList.MasterScanOrderCount)
{
// Did not find the next frag scan; find the previous frag scan
fragScanIndexMatch -= 1;
while (fragScanIndexMatch > 0 && scanList.MasterScanOrder[fragScanIndexMatch].ScanType == clsScanList.eScanTypeConstants.SurveyScan)
{
fragScanIndexMatch -= 1;
}
if (fragScanIndexMatch < 0)
{
fragScanIndexMatch = 0;
}
}
// This is a custom SIC-based parent ion
// Prior to August 2014, we set .FragScanIndices(0) = 0, which made it appear that the fragmentation scan was the first MS2 spectrum in the dataset for all custom SICs
// This caused undesirable display results in MASIC browser, so we now set it to the next MS2 scan that occurs after the survey scan (parent scan)
if (scanList.MasterScanOrder[fragScanIndexMatch].ScanType == clsScanList.eScanTypeConstants.FragScan)
{
currentParentIon.FragScanIndices.Add(scanList.MasterScanOrder[fragScanIndexMatch].ScanIndexPointer);
}
else
{
currentParentIon.FragScanIndices.Add(0);
}
}
currentParentIon.CustomSICPeak = true;
currentParentIon.CustomSICPeakComment = customMzSearchValue.Comment;
currentParentIon.CustomSICPeakMZToleranceDa = customMzSearchValue.MZToleranceDa;
currentParentIon.CustomSICPeakScanOrAcqTimeTolerance = customMzSearchValue.ScanOrAcqTimeTolerance;
if (currentParentIon.CustomSICPeakMZToleranceDa < double.Epsilon)
{
if (sicToleranceIsPPM)
{
currentParentIon.CustomSICPeakMZToleranceDa = clsUtilities.PPMToMass(defaultSICTolerance, currentParentIon.MZ);
}
else
{
currentParentIon.CustomSICPeakMZToleranceDa = defaultSICTolerance;
}
}
if (currentParentIon.CustomSICPeakScanOrAcqTimeTolerance < float.Epsilon)
{
currentParentIon.CustomSICPeakScanOrAcqTimeTolerance = defaultScanOrAcqTimeTolerance;
}
else
{
scanOrAcqTimeSumForAveraging += currentParentIon.CustomSICPeakScanOrAcqTimeTolerance;
scanOrAcqTimeSumCount += 1;
}
if (currentParentIon.SurveyScanIndex < scanList.SurveyScans.Count)
{
currentParentIon.OptimalPeakApexScanNumber =
scanList.SurveyScans[currentParentIon.SurveyScanIndex].ScanNumber;
}
else
{
currentParentIon.OptimalPeakApexScanNumber = 1;
}
currentParentIon.PeakApexOverrideParentIonIndex = -1;
scanList.ParentIons.Add(currentParentIon);
}
if (scanOrAcqTimeSumCount == CustomMZSearchValues.Count && scanOrAcqTimeSumForAveraging > 0)
{
// All of the entries had a custom scan or acq time tolerance defined
// Update mScanOrAcqTimeTolerance to the average of the values
ScanOrAcqTimeTolerance = (float)(Math.Round(scanOrAcqTimeSumForAveraging / scanOrAcqTimeSumCount, 4));
}
}
catch (Exception ex)
{
OnErrorEvent("Error in AddCustomSICValues", ex);
}
}
/// <summary>
/// Add the parent ion, or associate the fragmentation scan with an existing parent ion
///
/// Checks to see if the parent ion specified by surveyScanIndex and parentIonMZ exists in .ParentIons()
/// If mrmDaughterMZ is > 0, also considers that value when determining uniqueness
///
/// If the parent ion entry already exists, adds an entry to .FragScanIndices()
/// If it does not exist, adds a new entry to .ParentIons()
/// </summary>
/// <param name="scanList"></param>
/// <param name="surveyScanIndex">
/// If this is less than 0 the first MS2 scan(s) in the file occurred before we encountered a survey scan
/// In this case, we cannot properly associate the fragmentation scan with a survey scan
/// </param>
/// <param name="parentIonMZ"></param>
/// <param name="mrmDaughterMZ"></param>
/// <param name="mrmToleranceHalfWidth"></param>
/// <param name="fragScanIndex">This is typically equal to scanList.FragScans.Count - 1</param>
/// <param name="spectraCache"></param>
/// <param name="sicOptions"></param>
private void AddUpdateParentIons(
clsScanList scanList,
int surveyScanIndex,
double parentIonMZ,
double mrmDaughterMZ,
double mrmToleranceHalfWidth,
int fragScanIndex,
clsSpectraCache spectraCache,
clsSICOptions sicOptions)
{
const double MINIMUM_TOLERANCE_PPM = 0.01;
const double MINIMUM_TOLERANCE_DA = 0.0001;
var parentIonIndex = 0;
double parentIonTolerance;
if (sicOptions.SICToleranceIsPPM)
{
parentIonTolerance = sicOptions.SICTolerance / sicOptions.CompressToleranceDivisorForPPM;
if (parentIonTolerance < MINIMUM_TOLERANCE_PPM)
{
parentIonTolerance = MINIMUM_TOLERANCE_PPM;
}
}
else
{
parentIonTolerance = sicOptions.SICTolerance / sicOptions.CompressToleranceDivisorForDa;
if (parentIonTolerance < MINIMUM_TOLERANCE_DA)
{
parentIonTolerance = MINIMUM_TOLERANCE_DA;
}
}
// See if an entry exists yet in .ParentIons for the parent ion for this fragmentation scan
var matchFound = false;
if (mrmDaughterMZ > 0)
{
if (sicOptions.SICToleranceIsPPM)
{
// Force the tolerances to 0.01 m/z units
parentIonTolerance = MINIMUM_TOLERANCE_PPM;
}
else
{
// Force the tolerances to 0.01 m/z units
parentIonTolerance = MINIMUM_TOLERANCE_DA;
}
}
if (parentIonMZ > 0)
{
var parentIonToleranceDa = GetParentIonToleranceDa(sicOptions, parentIonMZ, parentIonTolerance);
for (parentIonIndex = scanList.ParentIons.Count - 1; parentIonIndex >= 0; parentIonIndex += -1)
{
if (scanList.ParentIons[parentIonIndex].SurveyScanIndex >= surveyScanIndex)
{
if (Math.Abs(scanList.ParentIons[parentIonIndex].MZ - parentIonMZ) <= parentIonToleranceDa)
{
if (mrmDaughterMZ < double.Epsilon ||
Math.Abs(scanList.ParentIons[parentIonIndex].MRMDaughterMZ - mrmDaughterMZ) <= parentIonToleranceDa)
{
matchFound = true;
break;
}
}
}
else
{
break;
}
}
}
if (!matchFound)
{
// Add a new parent ion entry to .ParentIons(), but only if surveyScanIndex is non-negative
if (surveyScanIndex < 0)
{
return;
}
var newParentIon = new clsParentIonInfo(parentIonMZ)
{
SurveyScanIndex = surveyScanIndex,
CustomSICPeak = false,
MRMDaughterMZ = mrmDaughterMZ,
MRMToleranceHalfWidth = mrmToleranceHalfWidth
};
newParentIon.FragScanIndices.Add(fragScanIndex);
newParentIon.OptimalPeakApexScanNumber = scanList.SurveyScans[surveyScanIndex].ScanNumber; // Was: .FragScans(fragScanIndex).ScanNumber
newParentIon.PeakApexOverrideParentIonIndex = -1;
scanList.FragScans[fragScanIndex].FragScanInfo.ParentIonInfoIndex = scanList.ParentIons.Count;
// Look for .MZ in the survey scan, using a tolerance of parentIonTolerance
// If found, then update the mass to the matched ion
// This is done to determine the parent ion mass more precisely
if (sicOptions.RefineReportedParentIonMZ)
{
if (FindClosestMZ(spectraCache, scanList.SurveyScans, surveyScanIndex, parentIonMZ, parentIonTolerance, out var parentIonMZMatch))
{
newParentIon.UpdateMz(parentIonMZMatch);
}
}
scanList.ParentIons.Add(newParentIon);
return;
}
// Add a new entry to .FragScanIndices() for the matching parent ion
// However, do not add a new entry if this is an MRM scan
if (mrmDaughterMZ < double.Epsilon)
{
scanList.ParentIons[parentIonIndex].FragScanIndices.Add(fragScanIndex);
scanList.FragScans[fragScanIndex].FragScanInfo.ParentIonInfoIndex = parentIonIndex;
}
}