public bool BuildLibrary(IProgressMonitor progress)
{
var bestSpectra = new List <SpectrumMzInfo>();
foreach (var nodePep in _doc.Peptides)
{
foreach (var nodeTranGroup in nodePep.TransitionGroups.Where(nodeTranGroup => nodeTranGroup.Results != null))
{
// For each precursor, export the spectrum with the highest TIC within peak boundaries
DbSpectrum bestSpectrum = null;
var bestDistance = double.MaxValue;
foreach (var result in nodeTranGroup.Results)
{
if (result.IsEmpty)
{
continue;
}
foreach (var resultsFile in result.Where(resultsFile => resultsFile.RetentionTime.HasValue))
{
foreach (var spectrum in _library.GetSpectraByPrecursor(null, nodeTranGroup.PrecursorMz))
{
var currentDistance = Math.Abs(spectrum.RetentionTime - resultsFile.RetentionTime.Value);
if (currentDistance < bestDistance)
{
bestSpectrum = spectrum;
bestDistance = currentDistance;
}
}
}
}
if (bestSpectrum != null)
{
bestSpectra.Add(new SpectrumMzInfo {
SourceFile = bestSpectrum.ResultsFile.FilePath,
PrecursorMz = bestSpectrum.PrecursorMz,
SpectrumPeaks = _library.LoadSpectrum(bestSpectrum),
Key = nodeTranGroup.GetLibKey(_doc.Settings, nodePep),
RetentionTimes = new[] { new SpectrumMzInfo.IonMobilityAndRT(bestSpectrum.ResultsFile.FilePath, IonMobilityAndCCS.EMPTY, bestSpectrum.RetentionTime, true) }.ToList()
});
}
}
}
using (var blibDb = BlibDb.CreateBlibDb(_libSpec.FilePath))
{
return(blibDb.CreateLibraryFromSpectra(new BiblioSpecLiteSpec(BLIB_NAME_INTERNAL, _libSpec.FilePath), bestSpectra, BLIB_NAME_INTERNAL, progress) != null);
}
}
public void ExportSpectralLibrary(string path, IProgressMonitor progressMonitor)
{
const string name = "exported";
var spectra = new Dictionary <LibKey, SpectrumMzInfo>();
foreach (var nodePepGroup in Document.MoleculeGroups)
{
foreach (var nodePep in nodePepGroup.Molecules)
{
foreach (var nodeTranGroup in nodePep.TransitionGroups)
{
for (var i = 0; i < Document.Settings.MeasuredResults.Chromatograms.Count; i++)
{
ProcessTransitionGroup(spectra, nodePepGroup, nodePep, nodeTranGroup, i);
}
}
}
}
var rCalcIrt = Document.Settings.HasRTPrediction
? Document.Settings.PeptideSettings.Prediction.RetentionTime.Calculator as RCalcIrt
: null;
IProgressStatus status = new ProgressStatus();
if (rCalcIrt != null && progressMonitor != null)
{
progressMonitor.UpdateProgress(status = status.ChangeSegments(0, 2));
}
using (var blibDb = BlibDb.CreateBlibDb(path))
{
var libSpec = new BiblioSpecLiteSpec(name, path);
blibDb.CreateLibraryFromSpectra(libSpec, spectra.Values.ToList(), name, progressMonitor, ref status);
}
if (rCalcIrt != null)
{
IrtDb.CreateIrtDb(path).AddPeptides(progressMonitor, rCalcIrt.GetDbIrtPeptides().ToList(), ref status);
}
}
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 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);
}