public bool Equals(PrecursorTextId other)
{
return(PrecursorMz.Equals(other.PrecursorMz) &&
Equals(IonMobility, other.IonMobility) &&
Equals(Target, other.Target) &&
Extractor == other.Extractor);
}
public SpectrumFilterPair(PrecursorTextId precursorTextId, Color peptideColor, int id, double?minTime, double?maxTime,
double highEnergyIonMobilityValueOffset, bool highAccQ1, bool highAccQ3)
{
Id = id;
ModifiedSequence = precursorTextId.Target;
PeptideColor = peptideColor;
Q1 = precursorTextId.PrecursorMz;
Extractor = precursorTextId.Extractor;
MinTime = minTime;
MaxTime = maxTime;
IonMobilityInfo = precursorTextId.IonMobility;
HighEnergyIonMobilityValueOffset = highEnergyIonMobilityValueOffset;
MinIonMobilityValue = IonMobilityInfo.IsEmpty ? null : IonMobilityInfo.IonMobility.Mobility - (IonMobilityInfo.IonMobilityExtractionWindowWidth ?? 0) / 2;
MaxIonMobilityValue = IonMobilityInfo.IsEmpty ? null : MinIonMobilityValue + (IonMobilityInfo.IonMobilityExtractionWindowWidth ?? 0);
HighAccQ1 = highAccQ1;
HighAccQ3 = highAccQ3;
Ms1ProductFilters = SimProductFilters = Ms2ProductFilters = EMPTY_FILTERS;
if (Q1 == 0)
{
Ms1ProductFilters = new[] { new SpectrumProductFilter(SignedMz.ZERO, 0) };
SimProductFilters = Ms1ProductFilters; // We want TIC and BPC for all scans, even if they have narrow machine settings and look like SIM
}
}
public SpectrumFilterPair(PrecursorTextId precursorTextId, Color peptideColor, int id, double?minTime, double?maxTime,
bool highAccQ1, bool highAccQ3)
{
Id = id;
ModifiedSequence = precursorTextId.Target;
PeptideColor = peptideColor;
Q1 = precursorTextId.PrecursorMz;
Extractor = precursorTextId.Extractor;
if (minTime.HasValue && maxTime.HasValue)
{
_filterByTime = true;
_minTime = minTime.Value;
_maxTime = maxTime.Value;
}
else
{
// If not min and max, then it should be neither. Asymmetric limits not supported.
Assume.IsTrue(!minTime.HasValue && !maxTime.HasValue);
}
IonMobilityInfo = precursorTextId.IonMobility;
MinIonMobilityValue = IonMobilityInfo.IsEmpty ? null : IonMobilityInfo.IonMobility.Mobility - (IonMobilityInfo.IonMobilityExtractionWindowWidth ?? 0) / 2;
MaxIonMobilityValue = IonMobilityInfo.IsEmpty ? null : MinIonMobilityValue + (IonMobilityInfo.IonMobilityExtractionWindowWidth ?? 0);
HighAccQ1 = highAccQ1;
HighAccQ3 = highAccQ3;
Ms1ProductFilters = SimProductFilters = Ms2ProductFilters = EMPTY_FILTERS;
if (Q1 == 0)
{
Ms1ProductFilters = new[] { new SpectrumProductFilter(SignedMz.ZERO, 0, 0) };
SimProductFilters = Ms1ProductFilters; // We want TIC and BPC for all scans, even if they have narrow machine settings and look like SIM
}
}
public SpectrumFilterPair(PrecursorTextId precursorTextId, Color peptideColor, int id, double?minTime, double?maxTime,
double?minDriftTimeMsec, double?maxDriftTimeMsec, double highEnergyDriftTimeOffsetMsec, bool highAccQ1, bool highAccQ3)
{
Id = id;
ModifiedSequence = precursorTextId.TextId;
PeptideColor = peptideColor;
Q1 = precursorTextId.PrecursorMz;
Extractor = precursorTextId.Extractor;
MinTime = minTime;
MaxTime = maxTime;
MinDriftTimeMsec = minDriftTimeMsec;
MaxDriftTimeMsec = maxDriftTimeMsec;
HighEnergyDriftTimeOffsetMsec = highEnergyDriftTimeOffsetMsec;
HighAccQ1 = highAccQ1;
HighAccQ3 = highAccQ3;
Ms1ProductFilters = SimProductFilters = Ms2ProductFilters = EMPTY_FILTERS;
if (Q1 == 0)
{
Ms1ProductFilters = new[] { new SpectrumProductFilter(0, 0) };
}
}
public SpectrumFilterPair(PrecursorTextId precursorTextId, Color peptideColor, int id, double?minTime, double?maxTime,
double?minIonMobilityValue, double?maxIonMobilityValue, IonMobilityAndCCS ionMobilityInfo, bool highAccQ1, bool highAccQ3)
{
Id = id;
ModifiedSequence = precursorTextId.Target;
PeptideColor = peptideColor;
Q1 = precursorTextId.PrecursorMz;
Extractor = precursorTextId.Extractor;
MinTime = minTime;
MaxTime = maxTime;
MinIonMobilityValue = minIonMobilityValue;
MaxIonMobilityValue = maxIonMobilityValue;
IonMobilityInfo = ionMobilityInfo ?? IonMobilityAndCCS.EMPTY;
HighAccQ1 = highAccQ1;
HighAccQ3 = highAccQ3;
Ms1ProductFilters = SimProductFilters = Ms2ProductFilters = EMPTY_FILTERS;
if (Q1 == 0)
{
Ms1ProductFilters = new[] { new SpectrumProductFilter(SignedMz.ZERO, 0) };
SimProductFilters = Ms1ProductFilters; // We want TIC and BPC for all scans, even if they have narrow machine settings and look like SIM
}
}
public IsotopeDistInfo(MassDistribution massDistribution,
TypedMass monoisotopicMass,
Adduct adduct,
Func <double, double> calcFilterWindow,
double massResolution,
double minimumAbundance)
{
_monoisotopicMass = monoisotopicMass;
_adduct = adduct.Unlabeled; // Don't reapply explicit isotope labels
// 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 = _adduct.MzFromNeutralMass(_monoisotopicMass);
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())
{
// This should never happen, but just in case it does happen, we safely exit the constructor
ExpectedPeaks = ImmutableList.Singleton(new MzRankProportion(monoMz, 0, 1.0f));
MonoMassIndex = BaseMassIndex = 0;
return;
}
var signedQ1FilterValues = q1FilterValues.Select(q => new SignedMz(q, adduct.AdductCharge < 0)).ToList();
// 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(signedQ1FilterValues[monoMassIndex], null, null, ChromExtractor.summed);
var filter = new SpectrumFilterPair(key, PeptideDocNode.UNKNOWN_COLOR, 0, null, null, false, false);
filter.AddQ1FilterValues(signedQ1FilterValues, calcFilterWindow);
var expectedSpectrum = filter.FilterQ1SpectrumList(new[] { new MsDataSpectrum
{
Mzs = massDistribution.Keys.ToArray(), Intensities = massDistribution.Values.ToArray(), NegativeCharge = (adduct.AdductCharge < 0)
} });
int startIndex = expectedSpectrum.Intensities.IndexOf(inten => inten >= minimumAbundance);
if (startIndex == -1)
{
// This can happen if the amino acid modifications are messed up,
// and the peptide mass is negative or something.
ExpectedPeaks = ImmutableList.Singleton(new MzRankProportion(monoMz, 0, 1.0f));
MonoMassIndex = BaseMassIndex = 0;
return;
}
// 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);
}
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;
}
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(SignedMz.ZERO, 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(SignedMz.ZERO, 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
var mz = new SignedMz(nodeGroup.PrecursorMz, nodeGroup.PrecursorCharge < 0);
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 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;
}
public bool Equals(PrecursorTextId other)
{
return(PrecursorMz.Equals(other.PrecursorMz) &&
string.Equals(TextId, other.TextId) &&
Extractor == other.Extractor);
}