private DbRefSpectra RefSpectrumFromPeaks(SpectrumMzInfo spectrum)
{
var peaksInfo = spectrum.SpectrumPeaks;
var refSpectra = new DbRefSpectra
{
PeptideSeq = FastaSequence.StripModifications(spectrum.Key.Sequence),
PrecursorMZ = spectrum.PrecursorMz,
PrecursorCharge = spectrum.Key.Charge,
PeptideModSeq = spectrum.Key.Sequence,
Copies = 1,
NumPeaks = (ushort)peaksInfo.Peaks.Length
};
refSpectra.Peaks = new DbRefSpectraPeaks
{
RefSpectra = refSpectra,
PeakIntensity = IntensitiesToBytes(peaksInfo.Peaks),
PeakMZ = MZsToBytes(peaksInfo.Peaks)
};
ModsFromModifiedSequence(refSpectra);
return(refSpectra);
}
public bool BuildLibrary(IProgressMonitor progress)
{
RetentionTimeRegression regr = null;
var standardSpectra = new List <SpectrumMzInfo>();
if (IrtStandard != null && !ReferenceEquals(IrtStandard, IrtStandard.EMPTY))
{
// Align Prosit iRTs with iRT standard
var standardPeptidesToAdd = SkylineWindow.ReadStandardPeptides(IrtStandard);
if (standardPeptidesToAdd != null && standardPeptidesToAdd.Count > 0)
{
// Get iRTs
var standardIRTMap = _rtModel.Predict(_prositClient, _document.Settings,
standardPeptidesToAdd.Select(p => (PrositRetentionTimeModel.PeptideDocNodeWrapper)p.NodePep).ToArray(),
CancellationToken.None);
var original = standardIRTMap.ToDictionary(p => p.Key.ModifiedTarget, p => p.Value);
var target = IrtStandard.Peptides.ToDictionary(p => p.ModifiedTarget, p => p.Irt);
var aligned = AlignedRetentionTimes.AlignLibraryRetentionTimes(target, original, 0.0, RegressionMethodRT.linear,
CancellationToken.None);
regr = aligned.Regression;
// Get spectra
var standardMS = _intensityModel.PredictBatches(_prositClient, progress, _document.Settings,
standardPeptidesToAdd.Select(p => p.WithNCE(_nce)).ToArray(),
CancellationToken.None);
// Merge iRT and MS2 into SpecMzInfos
standardSpectra = standardMS.Spectra.Select(m => m.SpecMzInfo).ToList();
for (var i = 0; i < standardSpectra.Count; ++i)
{
if (standardIRTMap.TryGetValue(standardMS.Spectra[i].PeptidePrecursorNCE.NodePep, out var iRT))
{
standardSpectra[i].RetentionTime = iRT;
}
}
}
}
// Predict fragment intensities
PrositMS2Spectra ms = _intensityModel.PredictBatches(_prositClient, progress, _document.Settings,
_peptides.Zip(_precursors,
(pep, prec) =>
new PrositIntensityModel.PeptidePrecursorNCE(pep, prec, _nce)).ToArray(),
CancellationToken.None);
var specMzInfo = ms.Spectra.Select(m => m.SpecMzInfo).ToList();
// Predict iRTs for peptides
var distinctPeps = _peptides.Select(p => (PrositRetentionTimeModel.PeptideDocNodeWrapper)p).Distinct(
new SystemLinqExtensionMethods.FuncEqualityComparer <PrositRetentionTimeModel.PeptideDocNodeWrapper>(
(p1, p2) => p1.Node.ModifiedSequence == p2.Node.ModifiedSequence)).ToArray();
var iRTMap = _rtModel.PredictBatches(_prositClient, progress, _document.Settings,
distinctPeps, CancellationToken.None);
for (var i = 0; i < specMzInfo.Count; ++i)
{
if (iRTMap.TryGetValue(ms.Spectra[i].PeptidePrecursorNCE.NodePep, out var iRT))
{
specMzInfo[i].RetentionTime = regr?.Conversion?.GetY(iRT) ?? iRT;
}
}
// Build library
var librarySpectra = SpectrumMzInfo.RemoveDuplicateSpectra(standardSpectra.Concat(specMzInfo).ToList());
// Delete if already exists, no merging with Prosit
var libraryExists = File.Exists(LibrarySpec.FilePath);
if (libraryExists)
{
var replace = _replaceLibrary();
if (!replace)
{
return(false);
}
FileEx.SafeDelete(LibrarySpec.FilePath);
}
if (!librarySpectra.Any())
{
return(true);
}
// Build the library
using (var blibDb = BlibDb.CreateBlibDb(LibrarySpec.FilePath))
{
var docLibrarySpec = new BiblioSpecLiteSpec(LibrarySpec.Name, LibrarySpec.FilePath);
BiblioSpecLiteLibrary docLibraryNew = null;
var docLibrarySpec2 = docLibrarySpec;
docLibraryNew =
blibDb.CreateLibraryFromSpectra(docLibrarySpec2, librarySpectra, LibrarySpec.Name, progress);
if (docLibraryNew == null)
{
return(false);
}
}
return(true);
}
private DbRefSpectra RefSpectrumFromPeaks(SpectrumMzInfo spectrum)
{
var peaksInfo = spectrum.SpectrumPeaks;
var refSpectra = new DbRefSpectra
{
PeptideSeq = FastaSequence.StripModifications(spectrum.Key.Sequence),
PrecursorMZ = spectrum.PrecursorMz,
PrecursorCharge = spectrum.Key.Charge,
PeptideModSeq = spectrum.Key.Sequence,
Copies = 1,
NumPeaks = (ushort)peaksInfo.Peaks.Length
};
refSpectra.Peaks = new DbRefSpectraPeaks
{
RefSpectra = refSpectra,
PeakIntensity = IntensitiesToBytes(peaksInfo.Peaks),
PeakMZ = MZsToBytes(peaksInfo.Peaks)
};
ModsFromModifiedSequence(refSpectra);
return refSpectra;
}
private bool BuildLibraryOrThrow(IProgressMonitor progress, ref IProgressStatus progressStatus)
{
progressStatus = progressStatus.ChangeSegments(0, 5);
var standardSpectra = new List <SpectrumMzInfo>();
// First get predictions for iRT standards specified by the user which may or may not be in the document
if (IrtStandard != null && !ReferenceEquals(IrtStandard, IrtStandard.EMPTY) && !ReferenceEquals(IrtStandard, IrtStandard.AUTO))
{
var standardPeptidesToAdd = ReadStandardPeptides(IrtStandard);
if (standardPeptidesToAdd != null && standardPeptidesToAdd.Count > 0)
{
// Get iRTs
var standardIRTMap = _rtModel.Predict(_prositClient, _document.Settings,
standardPeptidesToAdd.Select(p => (PrositRetentionTimeModel.PeptideDocNodeWrapper)p.NodePep).ToArray(),
CancellationToken.None);
// Get spectra
var standardMS = _intensityModel.PredictBatches(_prositClient, progress, ref progressStatus, _document.Settings,
standardPeptidesToAdd.Select(p => p.WithNCE(_nce)).ToArray(),
CancellationToken.None);
// Merge iRT and MS2 into SpecMzInfos
standardSpectra = standardMS.Spectra.Select(m => m.SpecMzInfo).ToList();
for (var i = 0; i < standardSpectra.Count; ++i)
{
if (standardIRTMap.TryGetValue(standardMS.Spectra[i].PeptidePrecursorNCE.NodePep, out var iRT))
{
standardSpectra[i].RetentionTime = iRT;
}
}
}
}
progressStatus = progressStatus.NextSegment();
// Predict fragment intensities
PrositMS2Spectra ms = _intensityModel.PredictBatches(_prositClient, progress, ref progressStatus, _document.Settings,
_peptides.Zip(_precursors,
(pep, prec) =>
new PrositIntensityModel.PeptidePrecursorNCE(pep, prec, IsotopeLabelType.light, _nce)).ToArray(),
CancellationToken.None);
progressStatus = progressStatus.NextSegment();
var specMzInfo = ms.Spectra.Select(m => m.SpecMzInfo).ToList();
// Predict iRTs for peptides
var distinctModifiedSequences = new HashSet <string>();
var distinctPeps = new List <PrositRetentionTimeModel.PeptideDocNodeWrapper>();
foreach (var p in _peptides)
{
if (distinctModifiedSequences.Add(p.ModifiedSequence))
{
distinctPeps.Add(new PrositRetentionTimeModel.PeptideDocNodeWrapper(p));
}
}
var iRTMap = _rtModel.PredictBatches(_prositClient, progress, ref progressStatus, _document.Settings,
distinctPeps, CancellationToken.None);
progressStatus = progressStatus.NextSegment();
for (var i = 0; i < specMzInfo.Count; ++i)
{
if (iRTMap.TryGetValue(ms.Spectra[i].PeptidePrecursorNCE.NodePep, out var iRT))
{
specMzInfo[i].RetentionTime = iRT;
}
}
// Build library
var librarySpectra = SpectrumMzInfo.RemoveDuplicateSpectra(standardSpectra.Concat(specMzInfo).ToList());
// Delete if already exists, no merging with Prosit
var libraryExists = File.Exists(LibrarySpec.FilePath);
if (libraryExists)
{
var replace = _replaceLibrary();
if (!replace)
{
return(false);
}
FileEx.SafeDelete(LibrarySpec.FilePath);
}
if (!librarySpectra.Any())
{
return(true);
}
progressStatus = progressStatus.NextSegment().ChangeMessage(Resources.SkylineWindow_SaveDocument_Saving___);
// Build the library
using (var blibDb = BlibDb.CreateBlibDb(LibrarySpec.FilePath))
{
var docLibrarySpec = new BiblioSpecLiteSpec(LibrarySpec.Name, LibrarySpec.FilePath);
BiblioSpecLiteLibrary docLibraryNew = null;
var docLibrarySpec2 = docLibrarySpec;
docLibraryNew =
blibDb.CreateLibraryFromSpectra(docLibrarySpec2, librarySpectra, LibrarySpec.Name, progress, ref progressStatus);
if (docLibraryNew == null)
{
return(false);
}
}
return(true);
}
private void ProcessTransitionGroup(IDictionary <LibKey, SpectrumMzInfo> spectra,
PeptideGroupDocNode nodePepGroup, PeptideDocNode nodePep, TransitionGroupDocNode nodeTranGroup, int replicateIndex)
{
LibKey key;
if (nodePep.IsProteomic)
{
var sequence = Document.Settings.GetPrecursorCalc(nodeTranGroup.TransitionGroup.LabelType, nodePep.ExplicitMods)
.GetModifiedSequence(nodePep.Peptide.Target, SequenceModFormatType.lib_precision, false);
key = new LibKey(sequence, nodeTranGroup.PrecursorAdduct.AdductCharge);
}
else
{
// For small molecules, the "modification" is expressed in the adduct
key = new LibKey(nodeTranGroup.CustomMolecule.GetSmallMoleculeLibraryAttributes(), nodeTranGroup.PrecursorAdduct);
}
var mi = new List <SpectrumPeaksInfo.MI>();
var rt = 0.0;
var im = IonMobilityAndCCS.EMPTY;
var imGroup = TransitionGroupIonMobilityInfo.EMPTY; // CCS may be available only at group level
var groupChromInfos = nodeTranGroup.GetSafeChromInfo(replicateIndex);
if (!groupChromInfos.IsEmpty)
{
var chromInfo = groupChromInfos.First(info => info.OptimizationStep == 0);
imGroup = chromInfo.IonMobilityInfo;
}
var maxApex = float.MinValue;
var maxApexMs1 = float.MinValue;
string chromFileName = null;
double?mobilityMs1 = null; // Track MS1 ion mobility in order to derive high energy ion mobility offset value
foreach (var nodeTran in nodeTranGroup.Transitions)
{
var chromInfos = nodeTran.GetSafeChromInfo(replicateIndex);
if (chromInfos.IsEmpty)
{
continue;
}
var chromInfo = chromInfos.First(info => info.OptimizationStep == 0);
if (chromInfo.Area == 0)
{
continue;
}
if (nodeTran.IsMs1)
{
// Track MS1 ion mobility in order to derive high energy ion mobility offset value
if (chromInfo.Height > maxApexMs1)
{
maxApexMs1 = chromInfo.Height;
mobilityMs1 = chromInfo.IonMobility.IonMobility.Mobility;
}
continue;
}
if (chromFileName == null)
{
var chromFileInfo = Document.Settings.MeasuredResults.Chromatograms[replicateIndex].MSDataFileInfos.FirstOrDefault(file => ReferenceEquals(file.Id, chromInfo.FileId));
if (chromFileInfo != null)
{
chromFileName = chromFileInfo.FilePath.GetFileName();
}
}
List <SpectrumPeakAnnotation> annotations = null;
if (nodeTran.Transition.IsNonReporterCustomIon()) // CONSIDER(bspratt) include annotation for all non-peptide-fragment transitions?
{
var smallMoleculeLibraryAttributes = nodeTran.Transition.CustomIon.GetSmallMoleculeLibraryAttributes();
var ion = new CustomIon(smallMoleculeLibraryAttributes, nodeTran.Transition.Adduct, nodeTran.GetMoleculeMass());
annotations = new List <SpectrumPeakAnnotation> {
SpectrumPeakAnnotation.Create(ion, nodeTran.Annotations.Note)
};
}
mi.Add(new SpectrumPeaksInfo.MI {
Mz = nodeTran.Mz, Intensity = chromInfo.Area, Quantitative = nodeTran.ExplicitQuantitative, Annotations = annotations
});
if (chromInfo.Height > maxApex)
{
maxApex = chromInfo.Height;
rt = chromInfo.RetentionTime;
var mobility = chromInfo.IonMobility.IonMobility;
var mobilityHighEnergyOffset = 0.0;
if (mobilityMs1.HasValue && mobility.HasValue && mobility.Mobility != mobilityMs1)
{
// Note any difference in MS1 and MS2 ion mobilities - the "high energy ion mobility offset"
mobilityHighEnergyOffset = mobility.Mobility.Value - mobilityMs1.Value;
mobility = mobility.ChangeIonMobility(mobilityMs1);
}
im = IonMobilityAndCCS.GetIonMobilityAndCCS(mobility, chromInfo.IonMobility.CollisionalCrossSectionSqA ?? imGroup.CollisionalCrossSection, mobilityHighEnergyOffset);
}
}
if (chromFileName == null)
{
return;
}
SpectrumMzInfo spectrumMzInfo;
if (!spectra.TryGetValue(key, out spectrumMzInfo))
{
spectrumMzInfo = new SpectrumMzInfo
{
SourceFile = DocumentFilePath,
Key = key,
PrecursorMz = nodeTranGroup.PrecursorMz,
SpectrumPeaks = new SpectrumPeaksInfo(mi.ToArray()),
RetentionTimes = new List <SpectrumMzInfo.IonMobilityAndRT>(),
IonMobility = im,
Protein = nodePepGroup.Name,
RetentionTime = rt
};
spectra[key] = spectrumMzInfo;
}
var isBest = replicateIndex == nodePep.BestResult;
if (isBest)
{
spectrumMzInfo.IonMobility = im;
spectrumMzInfo.RetentionTime = rt;
}
spectrumMzInfo.RetentionTimes.Add(new SpectrumMzInfo.IonMobilityAndRT(chromFileName, im, rt, isBest));
}
public TransitionGroupLibraryIrtTriple(SpectrumMzInfo spectrumInfo, TransitionGroupDocNode nodeGroup, double? irt, double precursorMz)
{
SpectrumInfo = spectrumInfo;
NodeGroup = nodeGroup;
Irt = irt;
PrecursorMz = precursorMz;
}
