/// <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);
}
public Dictionary <LibKey, DriftTimeInfo> FindDriftTimePeaks()
{
// Overwrite any existing measurements with newly derived ones
var measured = new Dictionary <LibKey, DriftTimeInfo>();
if (_existing != null && _existing.MeasuredDriftTimePeptides != null)
{
foreach (var existingPair in _existing.MeasuredDriftTimePeptides)
{
measured.Add(existingPair.Key, existingPair.Value);
}
}
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
//
_ms1DriftTimes = new Dictionary <LibKey, List <DriftTimeIntensityPair> >();
_ms2DriftTimes = new Dictionary <LibKey, List <DriftTimeIntensityPair> >();
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 drift times based on MS1 data
foreach (var dt in _ms1DriftTimes)
{
// Choose the drift time which gave the largest signal
var ms1DriftTime = dt.Value.OrderByDescending(p => p.Intensity).First().DriftTime;
// Check for MS2 data to use for high energy offset
List <DriftTimeIntensityPair> listDt;
var ms2DriftTime = _ms2DriftTimes.TryGetValue(dt.Key, out listDt)
? listDt.OrderByDescending(p => p.Intensity).First().DriftTime
: (ms1DriftTime ?? 0);
var value = new DriftTimeInfo(ms1DriftTime, ms2DriftTime - ms1DriftTime ?? 0);
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 dt in _ms2DriftTimes)
{
if (!_ms1DriftTimes.ContainsKey(dt.Key))
{
// Only MS2 drift times found, use that
var value = new DriftTimeInfo(dt.Value.OrderByDescending(p => p.Intensity).First().DriftTime, 0);
if (!measured.ContainsKey(dt.Key))
{
measured.Add(dt.Key, value);
}
else
{
measured[dt.Key] = value;
}
}
}
}
return(measured);
}
