/// <summary>
/// Looks through the result and finds ion mobility values.
/// Note that this method only returns new values that were found in results.
/// The returned dictionary should be merged with the existing values in
/// order to preserve those existing values.
/// </summary>
public Dictionary <LibKey, IonMobilityAndCCS> FindIonMobilityPeaks()
{
// Overwrite any existing measurements with newly derived ones
var measured = new Dictionary <LibKey, IonMobilityAndCCS>();
if (_document.Settings.MeasuredResults == null)
{
return(measured);
}
var filepaths = _document.Settings.MeasuredResults.MSDataFilePaths.ToArray();
_totalSteps = filepaths.Length * _document.MoleculeTransitionGroupCount;
if (_totalSteps == 0)
{
return(measured);
}
using (_msDataFileScanHelper = new MsDataFileScanHelper(SetScans, HandleLoadScanException))
{
//
// Avoid opening and re-opening raw files - make these the outer loop
//
_ms1IonMobilities = new Dictionary <LibKey, List <IonMobilityIntensityPair> >();
_ms2IonMobilities = new Dictionary <LibKey, List <IonMobilityIntensityPair> >();
var twopercent = (int)Math.Ceiling(_totalSteps * 0.02);
_totalSteps += twopercent;
_currentStep = twopercent;
if (_progressMonitor != null)
{
_progressStatus = new ProgressStatus(filepaths.First().GetFileName());
_progressStatus = _progressStatus.UpdatePercentCompleteProgress(_progressMonitor, _currentStep, _totalSteps); // Make that inital lag seem less dismal to the user
}
foreach (var fp in filepaths)
{
if (!ProcessFile(fp))
{
return(null); // User cancelled
}
}
// Find ion mobilities based on MS1 data
foreach (var dt in _ms1IonMobilities)
{
// Choose the ion mobility which gave the largest signal
// CONSIDER: average IM and CCS values that fall "near" the IM of largest signal?
var ms1IonMobility = dt.Value.OrderByDescending(p => p.Intensity).First().IonMobility;
// Check for MS2 data to use for high energy offset
List <IonMobilityIntensityPair> listDt;
var ms2IonMobility = _ms2IonMobilities.TryGetValue(dt.Key, out listDt)
? listDt.OrderByDescending(p => p.Intensity).First().IonMobility
: ms1IonMobility;
var value = IonMobilityAndCCS.GetIonMobilityAndCCS(ms1IonMobility.IonMobility, ms1IonMobility.CollisionalCrossSectionSqA, ms2IonMobility.IonMobility.Mobility.Value - ms1IonMobility.IonMobility.Mobility.Value);
if (!measured.ContainsKey(dt.Key))
{
measured.Add(dt.Key, value);
}
else
{
measured[dt.Key] = value;
}
}
// Check for data for which we have only MS2 to go on
foreach (var im in _ms2IonMobilities)
{
if (!_ms1IonMobilities.ContainsKey(im.Key))
{
// Only MS2 ion mobility values found, use that as a reasonable inference of MS1 ion mobility
var driftTimeIntensityPair = im.Value.OrderByDescending(p => p.Intensity).First();
var value = driftTimeIntensityPair.IonMobility;
// Note collisional cross section
if (_msDataFileScanHelper.ProvidesCollisionalCrossSectionConverter)
{
var mz = im.Key.PrecursorMz ?? GetMzFromDocument(im.Key);
var ccs = _msDataFileScanHelper.CCSFromIonMobility(value.IonMobility,
mz, im.Key.Charge);
if (ccs.HasValue)
{
value = IonMobilityAndCCS.GetIonMobilityAndCCS(value.IonMobility, ccs, value.HighEnergyIonMobilityValueOffset);
}
}
if (!measured.ContainsKey(im.Key))
{
measured.Add(im.Key, value);
}
else
{
measured[im.Key] = value;
}
}
}
}
return(measured);
}
private void EvaluateBestIonMobilityValue(int msLevel, LibKey libKey, float tolerance, List <TransitionFullScanInfo> transitions)
{
IonMobilityValue ionMobilityValue = IonMobilityValue.EMPTY;
double maxIntensity = 0;
// Avoid picking MS2 ion mobility values wildly different from MS1 valuess
IonMobilityValue ms1IonMobilityBest;
if ((msLevel == 2) && _ms1IonMobilities.ContainsKey(libKey))
{
ms1IonMobilityBest =
_ms1IonMobilities[libKey].OrderByDescending(p => p.Intensity)
.FirstOrDefault()
.IonMobility.IonMobility;
}
else
{
ms1IonMobilityBest = IonMobilityValue.EMPTY;
}
double maxHighEnergyDriftOffsetMsec = UseHighEnergyOffset ? 2 : 0; // CONSIDER(bspratt): user definable? or dynamically set by looking at scan to scan drift delta? Or resolving power?
foreach (var scan in _msDataFileScanHelper.MsDataSpectra.Where(scan => scan != null))
{
if (!scan.IonMobility.HasValue || !scan.Mzs.Any())
{
continue;
}
if (ms1IonMobilityBest.HasValue &&
(scan.IonMobility.Mobility <
ms1IonMobilityBest.Mobility - maxHighEnergyDriftOffsetMsec ||
scan.IonMobility.Mobility >
ms1IonMobilityBest.Mobility + maxHighEnergyDriftOffsetMsec))
{
continue;
}
// Get the total intensity for all transitions of current msLevel
double totalIntensity = 0;
foreach (var t in transitions)
{
Assume.IsTrue(t.ProductMz.IsNegative == scan.NegativeCharge); // It would be strange if associated scan did not have same polarity
var mzPeak = t.ProductMz;
var halfwin = (t.ExtractionWidth ?? tolerance) / 2;
var mzLow = mzPeak - halfwin;
var mzHigh = mzPeak + halfwin;
var first = Array.BinarySearch(scan.Mzs, mzLow);
if (first < 0)
{
first = ~first;
}
for (var i = first; i < scan.Mzs.Length; i++)
{
if (scan.Mzs[i] > mzHigh)
{
break;
}
totalIntensity += scan.Intensities[i];
}
}
if (maxIntensity < totalIntensity)
{
ionMobilityValue = scan.IonMobility;
maxIntensity = totalIntensity;
}
}
if (ionMobilityValue.HasValue)
{
var dict = (msLevel == 1) ? _ms1IonMobilities : _ms2IonMobilities;
var ccs = msLevel == 1 && _msDataFileScanHelper.ProvidesCollisionalCrossSectionConverter ? _msDataFileScanHelper.CCSFromIonMobility(ionMobilityValue, transitions.First().PrecursorMz, libKey.Charge) : null;
var result = new IonMobilityIntensityPair
{
IonMobility = IonMobilityAndCCS.GetIonMobilityAndCCS(ionMobilityValue, ccs, 0),
Intensity = maxIntensity
};
List <IonMobilityIntensityPair> listPairs;
if (!dict.TryGetValue(libKey, out listPairs))
{
listPairs = new List <IonMobilityIntensityPair>();
dict.Add(libKey, listPairs);
}
listPairs.Add(result);
}
}