private bool ProcessChromInfo(MsDataFileUri filePath, ChromatogramGroupInfo chromInfo, PeptidePrecursorPair pair,
TransitionGroupDocNode nodeGroup, float tolerance, LibKey libKey)
{
if (chromInfo.NumPeaks == 0) // Due to data polarity mismatch, probably
{
return(true);
}
Assume.IsTrue(chromInfo.BestPeakIndex != -1);
var resultIndex = _document.Settings.MeasuredResults.Chromatograms.IndexOf(c => c.GetFileInfo(filePath) != null);
if (resultIndex == -1)
{
return(true);
}
var chromFileInfo = _document.Settings.MeasuredResults.Chromatograms[resultIndex].GetFileInfo(filePath);
Assume.IsTrue(Equals(chromFileInfo.FilePath.GetLockMassParameters(), filePath.GetLockMassParameters()));
// Determine apex RT for DT measurement using most intense MS1 peak
var apexRT = GetApexRT(nodeGroup, resultIndex, chromFileInfo, true) ??
GetApexRT(nodeGroup, resultIndex, chromFileInfo, false);
if (!apexRT.HasValue)
{
return(true);
}
Assume.IsTrue(chromInfo.PrecursorMz.CompareTolerant(pair.NodeGroup.PrecursorMz, 1.0E-9f) == 0, @"mismatch in precursor values");
// Only use the transitions currently enabled
var transitionPointSets = chromInfo.TransitionPointSets.Where(
tp => nodeGroup.Transitions.Any(
t => (t.Mz - (tp.ExtractionWidth ?? tolerance) / 2) <= tp.ProductMz &&
(t.Mz + (tp.ExtractionWidth ?? tolerance) / 2) >= tp.ProductMz))
.ToArray();
for (var msLevel = 1; msLevel <= 2; msLevel++)
{
if (!ProcessMSLevel(filePath, msLevel, transitionPointSets, chromInfo, apexRT, nodeGroup, libKey, tolerance))
{
return(false); // User cancelled
}
}
return(true);
}
private bool ProcessChromInfo(MsDataFileUri filePath, ChromatogramGroupInfo chromInfo, PeptidePrecursorPair pair,
TransitionGroupDocNode nodeGroup, float tolerance, LibKey libKey)
{
Assume.IsTrue(chromInfo.BestPeakIndex != -1);
var resultIndex = _document.Settings.MeasuredResults.Chromatograms.IndexOf(c => c.GetFileInfo(filePath) != null);
if (resultIndex == -1)
return true;
var chromFileInfo = _document.Settings.MeasuredResults.Chromatograms[resultIndex].GetFileInfo(filePath);
Assume.IsTrue(Equals(chromFileInfo.FilePath.GetLockMassParameters(), filePath.GetLockMassParameters()));
// Determine apex RT for DT measurement using most intense MS1 peak
var apexRT = GetApexRT(nodeGroup, resultIndex, chromFileInfo, true) ??
GetApexRT(nodeGroup, resultIndex, chromFileInfo, false);
Assume.IsTrue(chromInfo.PrecursorMz == pair.NodeGroup.PrecursorMz);
// Only use the transitions currently enabled
var transitionPointSets = chromInfo.TransitionPointSets.Where(
tp => nodeGroup.Transitions.Any(
t => (t.Mz - (tp.ExtractionWidth ?? tolerance)/2) <= tp.ProductMz &&
(t.Mz + (tp.ExtractionWidth ?? tolerance)/2) >= tp.ProductMz))
.ToArray();
for (var msLevel = 1; msLevel <= 2; msLevel++)
{
if (!ProcessMSLevel(filePath, msLevel, transitionPointSets, chromInfo, apexRT, nodeGroup, libKey, tolerance))
return false; // User cancelled
}
return true;
}
