public SpectrumFilter(SrmDocument document, MsDataFileUri msDataFileUri, IFilterInstrumentInfo instrumentInfo,
IRetentionTimePredictor retentionTimePredictor = null, bool firstPass = false)
{
_fullScan = document.Settings.TransitionSettings.FullScan;
_instrument = document.Settings.TransitionSettings.Instrument;
_acquisitionMethod = _fullScan.AcquisitionMethod;
if (instrumentInfo != null)
_isWatersFile = instrumentInfo.IsWatersFile;
IsFirstPass = firstPass;
var comparer = PrecursorTextId.PrecursorTextIdComparerInstance;
var dictPrecursorMzToFilter = new SortedDictionary<PrecursorTextId, SpectrumFilterPair>(comparer);
if (EnabledMs || EnabledMsMs)
{
if (EnabledMs)
{
_isHighAccMsFilter = !Equals(_fullScan.PrecursorMassAnalyzer,
FullScanMassAnalyzerType.qit);
if (!firstPass)
{
var key = new PrecursorTextId(0, null, ChromExtractor.summed); // TIC
dictPrecursorMzToFilter.Add(key, new SpectrumFilterPair(key, PeptideDocNode.UNKNOWN_COLOR, dictPrecursorMzToFilter.Count,
_instrument.MinTime, _instrument.MaxTime, null, null, 0, _isHighAccMsFilter, _isHighAccProductFilter));
key = new PrecursorTextId(0, null, ChromExtractor.base_peak); // BPC
dictPrecursorMzToFilter.Add(key, new SpectrumFilterPair(key, PeptideDocNode.UNKNOWN_COLOR, dictPrecursorMzToFilter.Count,
_instrument.MinTime, _instrument.MaxTime, null, null, 0, _isHighAccMsFilter, _isHighAccProductFilter));
}
}
if (EnabledMsMs)
{
_isHighAccProductFilter = !Equals(_fullScan.ProductMassAnalyzer,
FullScanMassAnalyzerType.qit);
if (_fullScan.AcquisitionMethod == FullScanAcquisitionMethod.DIA &&
_fullScan.IsolationScheme.IsAllIons)
{
if (instrumentInfo != null)
{
_isWatersMse = _isWatersFile;
_isAgilentMse = instrumentInfo.IsAgilentFile;
}
_mseLevel = 1;
}
}
Func<double, double> calcWindowsQ1 = _fullScan.GetPrecursorFilterWindow;
Func<double, double> calcWindowsQ3 = _fullScan.GetProductFilterWindow;
_minTime = _instrument.MinTime;
_maxTime = _instrument.MaxTime;
bool canSchedule = CanSchedule(document, retentionTimePredictor);
// TODO: Figure out a way to turn off time sharing on first SIM scan so that
// times can be shared for MS1 without SIM scans
_isSharedTime = !canSchedule;
// If we're using bare measured drift times from spectral libraries, go get those now
var libraryIonMobilityInfo = document.Settings.PeptideSettings.Prediction.UseLibraryDriftTimes
? document.Settings.GetIonMobilities(msDataFileUri)
: null;
foreach (var nodePep in document.Molecules)
{
if (firstPass && !retentionTimePredictor.IsFirstPassPeptide(nodePep))
continue;
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
if (nodeGroup.Children.Count == 0)
continue;
double? minTime = _minTime, maxTime = _maxTime;
double? startDriftTimeMsec = null, endDriftTimeMsec = null;
double windowDT;
double highEnergyDriftTimeOffsetMsec = 0;
DriftTimeInfo centerDriftTime = document.Settings.PeptideSettings.Prediction.GetDriftTime(
nodePep, nodeGroup, libraryIonMobilityInfo, out windowDT);
if (centerDriftTime.DriftTimeMsec(false).HasValue)
{
startDriftTimeMsec = centerDriftTime.DriftTimeMsec(false) - windowDT / 2; // Get the low energy drift time
endDriftTimeMsec = startDriftTimeMsec + windowDT;
highEnergyDriftTimeOffsetMsec = centerDriftTime.HighEnergyDriftTimeOffsetMsec;
}
if (canSchedule)
{
if (RetentionTimeFilterType.scheduling_windows == _fullScan.RetentionTimeFilterType)
{
double? centerTime = null;
double windowRT = 0;
if (retentionTimePredictor != null)
{
centerTime = retentionTimePredictor.GetPredictedRetentionTime(nodePep);
}
else
{
var prediction = document.Settings.PeptideSettings.Prediction;
if (prediction.RetentionTime == null || !prediction.RetentionTime.IsAutoCalculated)
{
centerTime = document.Settings.PeptideSettings.Prediction.PredictRetentionTimeForChromImport(
document, nodePep, nodeGroup, out windowRT);
}
}
// Force the center time to be at least zero
if (centerTime.HasValue && centerTime.Value < 0)
centerTime = 0;
if (_fullScan.RetentionTimeFilterLength != 0)
{
windowRT = _fullScan.RetentionTimeFilterLength * 2;
}
if (centerTime != null)
{
double startTime = centerTime.Value - windowRT / 2;
double endTime = startTime + windowRT;
minTime = Math.Max(minTime ?? 0, startTime);
maxTime = Math.Min(maxTime ?? double.MaxValue, endTime);
}
}
else if (RetentionTimeFilterType.ms2_ids == _fullScan.RetentionTimeFilterType)
{
var times = document.Settings.GetBestRetentionTimes(nodePep, msDataFileUri);
if (times.Length > 0)
{
minTime = Math.Max(minTime ?? 0, times.Min() - _fullScan.RetentionTimeFilterLength);
maxTime = Math.Min(maxTime ?? double.MaxValue, times.Max() + _fullScan.RetentionTimeFilterLength);
}
}
}
SpectrumFilterPair filter;
string textId = nodePep.RawTextId; // Modified Sequence for peptides, or some other string for custom ions
double mz = nodeGroup.PrecursorMz;
var key = new PrecursorTextId(mz, textId, ChromExtractor.summed);
if (!dictPrecursorMzToFilter.TryGetValue(key, out filter))
{
filter = new SpectrumFilterPair(key, nodePep.Color, dictPrecursorMzToFilter.Count, minTime, maxTime,
startDriftTimeMsec, endDriftTimeMsec, highEnergyDriftTimeOffsetMsec,
_isHighAccMsFilter, _isHighAccProductFilter);
dictPrecursorMzToFilter.Add(key, filter);
}
if (!EnabledMs)
{
filter.AddQ3FilterValues(from TransitionDocNode nodeTran in nodeGroup.Children
select nodeTran.Mz, calcWindowsQ3);
}
else if (!EnabledMsMs)
{
filter.AddQ1FilterValues(GetMS1MzValues(nodeGroup), calcWindowsQ1);
}
else
{
filter.AddQ1FilterValues(GetMS1MzValues(nodeGroup), calcWindowsQ1);
filter.AddQ3FilterValues(from TransitionDocNode nodeTran in nodeGroup.Children
where !nodeTran.IsMs1
select nodeTran.Mz, calcWindowsQ3);
}
}
}
_filterMzValues = dictPrecursorMzToFilter.Values.ToArray();
var listChromKeyFilterIds = new List<ChromKey>();
foreach (var spectrumFilterPair in _filterMzValues)
{
spectrumFilterPair.AddChromKeys(listChromKeyFilterIds);
}
_productChromKeys = listChromKeyFilterIds.ToArray();
// Sort a copy of the filter pairs by maximum retention time so that we can detect when
// filters are no longer active.
_filterRTValues = new SpectrumFilterPair[_filterMzValues.Length];
Array.Copy(_filterMzValues, _filterRTValues, _filterMzValues.Length);
Array.Sort(_filterRTValues, CompareByRT);
}
InitRTLimits();
}
public void ProcessExtractedSpectrum(float time, SpectraChromDataProvider.Collectors chromatograms, int scanId, ExtractedSpectrum spectrum, Action<int, ChromCollector> addCollector)
{
double precursorMz = spectrum.PrecursorMz;
double? ionMobilityValue = spectrum.IonMobilityValue;
double ionMobilityExtractionWidth = spectrum.IonMobilityExtractionWidth;
string textId = spectrum.TextId;
ChromExtractor extractor = spectrum.Extractor;
int ionScanCount = spectrum.ProductFilters.Length;
ChromDataCollector collector;
var key = new PrecursorTextId(precursorMz, textId, extractor);
int index = spectrum.FilterIndex;
while (PrecursorCollectorMap.Count <= index)
PrecursorCollectorMap.Add(null);
if (PrecursorCollectorMap[index] != null)
collector = PrecursorCollectorMap[index].Item2;
else
{
collector = new ChromDataCollector(textId, precursorMz, ionMobilityValue, ionMobilityExtractionWidth, index, IsGroupedTime);
PrecursorCollectorMap[index] = new Tuple<PrecursorTextId, ChromDataCollector>(key, collector);
}
int ionCount = collector.ProductIntensityMap.Count;
if (ionCount == 0)
ionCount = ionScanCount;
// Add new time to the shared time list if not SRM, which doesn't share times, or
// the times are shared with the entire set, as in MS1
int lenTimes = collector.TimeCount;
if (IsGroupedTime)
{
// Shared scan ids and times do not belong to a group.
collector.AddScanId(scanId);
collector.AddGroupedTime(time);
lenTimes = collector.GroupedTimesCollector.Count;
}
// Add intensity values to ion scans
for (int j = 0; j < ionScanCount; j++)
{
var productFilter = spectrum.ProductFilters[j];
var chromIndex = chromatograms.ProductFilterIdToId(productFilter.FilterId);
ChromCollector chromCollector;
if (!collector.ProductIntensityMap.TryGetValue(productFilter, out chromCollector))
{
chromCollector = new ChromCollector(chromIndex, IsSingleTime, spectrum.MassErrors != null);
// If more than a single ion scan, add any zeros necessary
// to make this new chromatogram have an entry for each time.
if (ionScanCount > 1 && lenTimes > 1)
chromCollector.FillIntensities(chromIndex, lenTimes - 1, _blockWriter);
collector.ProductIntensityMap.Add(productFilter, chromCollector);
if (addCollector != null)
addCollector(productFilter.FilterId, chromCollector);
}
if (IsSingleTime)
chromCollector.AddTime(chromIndex, time, _blockWriter);
if (spectrum.MassErrors != null)
chromCollector.AddMassError(chromIndex, spectrum.MassErrors[j], _blockWriter);
chromCollector.AddIntensity(chromIndex, spectrum.Intensities[j], _blockWriter);
}
// Add data for chromatogram graph.
if (_allChromData != null && spectrum.PrecursorMz != 0) // Exclude TIC and BPC
_allChromData.Add(spectrum.TextId, spectrum.PeptideColor, spectrum.FilterIndex, time, spectrum.Intensities);
// If this was a multiple ion scan and not all ions had measurements,
// make sure missing ions have zero intensities in the chromatogram.
if (ionScanCount > 1 &&
(ionCount != ionScanCount || ionCount != collector.ProductIntensityMap.Count))
{
// Times should have gotten one longer
foreach (var item in collector.ProductIntensityMap)
{
var productFilter = item.Key;
var chromCollector = item.Value;
var chromIndex = chromatograms.ProductFilterIdToId(productFilter.FilterId);
if (chromCollector.Count < lenTimes)
chromCollector.AddIntensity(chromIndex, 0, _blockWriter);
}
}
}
public IsotopeDistInfo(MassDistribution massDistribution,
double monoisotopicMass,
bool isMassH, // Is monoisotopicMass M+H, or just M as in small molecule use?
int charge,
Func<double, double> calcFilterWindow,
double massResolution,
double minimumAbundance)
{
_monoisotopicMass = monoisotopicMass;
_charge = charge;
_isMassH = isMassH;
// Get peak center of mass values for the given resolution
var q1FilterValues = MassDistribution.NewInstance(massDistribution, massResolution, 0).Keys.ToList();
// Find the monoisotopic m/z and make sure it is exactly the expected number
double monoMz = isMassH ? SequenceMassCalc.GetMZ(_monoisotopicMass, _charge) : BioMassCalc.CalculateIonMz(_monoisotopicMass, _charge);
double monoMzDist = monoMz;
int monoMassIndex = 0;
for (int i = 0; i < q1FilterValues.Count; i++)
{
double peakCenterMz = q1FilterValues[i];
double filterWindow = calcFilterWindow(peakCenterMz);
double startMz = peakCenterMz - filterWindow/2;
double endMz = startMz + filterWindow;
if (startMz < monoMz && monoMz < endMz)
{
monoMzDist = q1FilterValues[i];
q1FilterValues[i] = monoMz;
monoMassIndex = i;
break;
}
}
// Insert a M-1 peak, even if it is not expected in the isotope mass distribution
if (monoMassIndex == 0 && q1FilterValues.Count > 1)
{
// Use the delta from the original distribution monoMz to the next peak
q1FilterValues.Insert(0, monoMz + monoMzDist - q1FilterValues[1]);
monoMassIndex++;
}
if (!q1FilterValues.Any()) // As is small molecule docs with mz values only, no formulas
return;
// Use the filtering algorithm that will be used on real data to determine the
// expected proportions of the mass distribution that will end up filtered into
// peaks
// CONSIDER: Mass accuracy information is not calculated here
var key = new PrecursorTextId(q1FilterValues[monoMassIndex], null, ChromExtractor.summed);
var filter = new SpectrumFilterPair(key, PeptideDocNode.UNKNOWN_COLOR, 0, null, null, null, null, 0, false, false);
filter.AddQ1FilterValues(q1FilterValues, calcFilterWindow);
var expectedSpectrum = filter.FilterQ1SpectrumList(new[] { new MsDataSpectrum
{ Mzs = massDistribution.Keys.ToArray(), Intensities = massDistribution.Values.ToArray() } });
int startIndex = expectedSpectrum.Intensities.IndexOf(inten => inten >= minimumAbundance);
if (startIndex == -1)
{
throw new InvalidOperationException(
string.Format(Resources.IsotopeDistInfo_IsotopeDistInfo_Minimum_abundance__0__too_high,
minimumAbundance));
}
// Always include the M-1 peak, even if it is expected to have zero intensity
if (startIndex > monoMassIndex - 1)
startIndex = monoMassIndex - 1;
if (startIndex < 0)
startIndex = 0;
int endIndex = expectedSpectrum.Intensities.LastIndexOf(inten => inten >= minimumAbundance) + 1;
int countPeaks = endIndex - startIndex;
var listProportionIndices = new List<KeyValuePair<float, int>>(countPeaks);
for (int i = 0; i < countPeaks; i++)
{
listProportionIndices.Add(new KeyValuePair<float, int>(
expectedSpectrum.Intensities[i + startIndex], i));
}
// Sort proportions descending.
listProportionIndices.Sort((p1, p2) => Comparer.Default.Compare(p2.Key, p1.Key));
// Set proportions and ranks back in the original locations
var expectedProportionRanks = new KeyValuePair<float, int>[countPeaks];
for (int i = 0; i < countPeaks; i++)
{
expectedProportionRanks[listProportionIndices[i].Value] =
new KeyValuePair<float, int>(listProportionIndices[i].Key, i + 1);
}
// TODO: Can this be discarded?
// MassDistribution = massDistribution;
MonoMassIndex = monoMassIndex - startIndex;
// Find the base peak and fill in the masses and proportions
var expectedPeaks = new List<MzRankProportion>();
for (int i = 0; i < countPeaks; i++)
{
float expectedProportion = expectedProportionRanks[i].Key;
int rank = expectedProportionRanks[i].Value;
expectedPeaks.Add(new MzRankProportion(q1FilterValues[i + startIndex], rank, expectedProportion));
if (expectedProportion > expectedProportionRanks[BaseMassIndex].Key)
BaseMassIndex = i;
}
ExpectedPeaks = expectedPeaks;
}