/// <summary>
/// Constructor for a MS2 scan
/// </summary>
public clsScanInfo(double fragScanParentIonMz)
{
MRMScanType = MRMScanTypeConstants.NotMRM;
FragScanInfo = new clsFragScanInfo(fragScanParentIonMz);
MRMScanInfo = new clsMRMScanInfo();
ExtendedHeaderInfo = new Dictionary <int, string>();
}
private bool MRMParentDaughterMatch(
udtSRMListType udtSRMListEntry,
clsMRMScanInfo mrmSettingsEntry,
int mrmMassIndex)
{
return(MRMParentDaughterMatch(
udtSRMListEntry.ParentIonMZ,
udtSRMListEntry.CentralMass,
mrmSettingsEntry.ParentIonMZ,
mrmSettingsEntry.MRMMassList[mrmMassIndex].CentralMass));
}
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);
}
/// <summary>
/// Add the parent ion, or associate the fragmentation scan with an existing parent ion
/// </summary>
/// <param name="scanList"></param>
/// <param name="surveyScanIndex"></param>
/// <param name="parentIonMZ"></param>
/// <param name="mrmInfo"></param>
/// <param name="spectraCache"></param>
/// <param name="sicOptions"></param>
public void AddUpdateParentIons(
clsScanList scanList,
int surveyScanIndex,
double parentIonMZ,
clsMRMScanInfo mrmInfo,
clsSpectraCache spectraCache,
clsSICOptions sicOptions)
{
for (var mrmIndex = 0; mrmIndex < mrmInfo.MRMMassCount; mrmIndex++)
{
var mrmDaughterMZ = mrmInfo.MRMMassList[mrmIndex].CentralMass;
var mrmToleranceHalfWidth = Math.Round((mrmInfo.MRMMassList[mrmIndex].EndMass - mrmInfo.MRMMassList[mrmIndex].StartMass) / 2, 6);
if (mrmToleranceHalfWidth < 0.001)
{
mrmToleranceHalfWidth = 0.001;
}
AddUpdateParentIons(scanList, surveyScanIndex, parentIonMZ, mrmDaughterMZ, mrmToleranceHalfWidth, scanList.FragScans.Count - 1, spectraCache, sicOptions);
}
}
/// <summary>
/// Duplicate MRM info
/// </summary>
/// <param name="sourceInfo"></param>
/// <returns></returns>
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 <udtMRMMassRangeType>();
}
else
{
targetInfo.MRMMassList = new List <udtMRMMassRangeType>(sourceInfo.MRMMassList.Count);
targetInfo.MRMMassList.AddRange(sourceInfo.MRMMassList);
}
return(targetInfo);
}
/// <summary>
/// Duplicate MRM info, overriding the parent ion m/z using parentIonMZ
/// </summary>
/// <param name="sourceInfo"></param>
/// <param name="parentIonMZ"></param>
/// <returns></returns>
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 <udtMRMMassRangeType>();
}
else
{
targetInfo.MRMMassList = new List <udtMRMMassRangeType>(sourceInfo.MRMMassList.Count);
targetInfo.MRMMassList.AddRange(sourceInfo.MRMMassList);
}
return(targetInfo);
}