public static void SetStandards(IEnumerable <DbIrtPeptide> peptides, IrtStandard standard)
{
SetStandards(peptides, standard.Peptides.Select(pep => pep.ModifiedTarget));
}
public static ProcessedIrtAverages ProcessRetentionTimes(IProgressMonitor monitor,
IRetentionTimeProvider[] providers, DbIrtPeptide[] standardPeptideList, DbIrtPeptide[] items)
{
var matchedStandard = IrtStandard.WhichStandard(standardPeptideList.Select(pep => pep.ModifiedTarget));
if (matchedStandard != null)
{
var dummyDoc = new SrmDocument(SrmSettingsList.GetDefault());
using (var reader = matchedStandard.GetDocumentReader())
{
if (reader != null)
{
dummyDoc = dummyDoc.ImportDocumentXml(reader,
string.Empty,
MeasuredResults.MergeAction.remove,
false,
null,
Settings.Default.StaticModList,
Settings.Default.HeavyModList,
null,
out _,
out _,
false);
standardPeptideList = standardPeptideList.Select(pep => new DbIrtPeptide(pep)).ToArray();
foreach (var dummyPep in dummyDoc.Molecules.Where(pep => pep.HasExplicitMods))
{
var standardPepIdx = standardPeptideList.IndexOf(pep => dummyPep.ModifiedTarget.Equals(pep.ModifiedTarget));
standardPeptideList[standardPepIdx] = new DbIrtPeptide(standardPeptideList[standardPepIdx])
{
ModifiedTarget = dummyDoc.Settings.GetModifiedSequence(dummyPep.ModifiedTarget, IsotopeLabelType.heavy, dummyPep.ExplicitMods)
};
}
}
}
}
IProgressStatus status = new ProgressStatus(Resources.LibraryGridViewDriver_ProcessRetentionTimes_Adding_retention_times);
var dictPeptideAverages = new Dictionary <Target, IrtPeptideAverages>();
var providerData = new List <RetentionTimeProviderData>();
var runCount = 0;
foreach (var retentionTimeProvider in providers)
{
if (monitor.IsCanceled)
{
return(null);
}
monitor.UpdateProgress(status = status.ChangeMessage(string.Format(
Resources.LibraryGridViewDriver_ProcessRetentionTimes_Converting_retention_times_from__0__,
retentionTimeProvider.Name)));
runCount++;
var data = new RetentionTimeProviderData(retentionTimeProvider, standardPeptideList);
if (data.RegressionSuccess || data.CalcRegressionWith(retentionTimeProvider, standardPeptideList, items))
{
AddRetentionTimesToDict(retentionTimeProvider, data.RegressionRefined, dictPeptideAverages, standardPeptideList);
}
providerData.Add(data);
monitor.UpdateProgress(status = status.ChangePercentComplete(runCount * 100 / providers.Length));
}
monitor.UpdateProgress(status.Complete());
return(new ProcessedIrtAverages(dictPeptideAverages, providerData));
}
public List <DbIrtPeptide> RecalibrateStandards(DbIrtPeptide[] standardPeptideList)
{
var peptideAllIrtTimes = new Dictionary <Target, List <Tuple <double, double> > >(); // peptide -> list of (irt, time)
foreach (var data in ProviderData)
{
foreach (var peptide in data.FilteredPeptides)
{
if (!peptideAllIrtTimes.TryGetValue(peptide.Target, out var pepTimes))
{
pepTimes = new List <Tuple <double, double> >();
peptideAllIrtTimes[peptide.Target] = pepTimes;
}
pepTimes.Add(Tuple.Create(peptide.Irt, peptide.RetentionTime.Value));
}
}
var peptideBestIrtTimes = new Dictionary <Target, Tuple <double, double> >(); // peptide -> (percentile irt, percentile time)
foreach (var peptide in peptideAllIrtTimes)
{
var statIrts = new Statistics(peptide.Value.Select(p => p.Item1));
var statTimes = new Statistics(peptide.Value.Select(p => p.Item2));
var percentile = IrtStandard.GetSpectrumTimePercentile(peptide.Key);
peptideBestIrtTimes[peptide.Key] = Tuple.Create(statIrts.Percentile(percentile), statTimes.Percentile(percentile));
}
DbIrtPeptide min = null, max = null;
foreach (var standard in standardPeptideList) // loop over list of standard peptides to find min/max that we have values for
{
if ((min == null || standard.Irt < min.Irt) && peptideBestIrtTimes.ContainsKey(standard.ModifiedTarget))
{
min = standard;
}
if ((max == null || standard.Irt > max.Irt) && peptideBestIrtTimes.ContainsKey(standard.ModifiedTarget))
{
max = standard;
}
}
if (min == null || max == null)
{
throw new Exception(Resources.EditIrtCalcDlg_RecalibrateStandards_Could_not_get_a_minimum_or_maximum_standard_peptide_);
}
var statX = new Statistics(peptideBestIrtTimes[min.ModifiedTarget].Item2, peptideBestIrtTimes[max.ModifiedTarget].Item2);
var statY = new Statistics(peptideBestIrtTimes[min.ModifiedTarget].Item1, peptideBestIrtTimes[max.ModifiedTarget].Item1);
var line = new RegressionLine(statY.Slope(statX), statY.Intercept(statX));
var newStandardPeptideList = new List <DbIrtPeptide>();
foreach (var peptide in standardPeptideList)
{
if (!peptideBestIrtTimes.TryGetValue(peptide.ModifiedTarget, out var times))
{
throw new Exception(Resources.ProcessedIrtAverages_RecalibrateStandards_A_standard_peptide_was_missing_when_trying_to_recalibrate_);
}
newStandardPeptideList.Add(new DbIrtPeptide(peptide)
{
Irt = line.GetY(times.Item2)
});
}
return(newStandardPeptideList);
}
public static ProcessedIrtAverages ProcessRetentionTimes(IProgressMonitor monitor,
IRetentionTimeProvider[] providers, DbIrtPeptide[] standardPeptideList, DbIrtPeptide[] items, IrtRegressionType regressionType)
{
var heavyStandards = new DbIrtPeptide[standardPeptideList.Length];
var matchedStandard = IrtStandard.WhichStandard(standardPeptideList.Select(pep => pep.ModifiedTarget));
if (matchedStandard != null && matchedStandard.HasDocument)
{
// Check embedded standard document for known standard to determine if the standard peptides should be heavy
// Import iRT standard document into an empty document (rather than just getting the document), because importing also imports the modifications
var standardDoc = matchedStandard.ImportTo(new SrmDocument(SrmSettingsList.GetDefault()));
standardPeptideList = standardPeptideList.Select(pep => new DbIrtPeptide(pep)).ToArray();
foreach (var dummyPep in standardDoc.Molecules.Where(pep => pep.HasExplicitMods))
{
var standardPepIdx = standardPeptideList.IndexOf(pep => dummyPep.ModifiedTarget.Equals(pep.ModifiedTarget));
if (standardPepIdx < 0)
{
continue;
}
var heavyTarget = standardDoc.Settings.GetModifiedSequence(dummyPep.ModifiedTarget, IsotopeLabelType.heavy, dummyPep.ExplicitMods);
if (!standardPeptideList[standardPepIdx].ModifiedTarget.Equals(heavyTarget))
{
heavyStandards[standardPepIdx] = new DbIrtPeptide(standardPeptideList[standardPepIdx])
{
ModifiedTarget = heavyTarget
}
}
;
}
}
IProgressStatus status = new ProgressStatus(Resources.LibraryGridViewDriver_ProcessRetentionTimes_Adding_retention_times);
var dictPeptideAverages = new Dictionary <Target, IrtPeptideAverages>();
var providerData = new List <RetentionTimeProviderData>();
var runCount = 0;
foreach (var retentionTimeProvider in providers)
{
if (monitor.IsCanceled)
{
return(null);
}
monitor.UpdateProgress(status = status.ChangeMessage(string.Format(
Resources.LibraryGridViewDriver_ProcessRetentionTimes_Converting_retention_times_from__0__,
retentionTimeProvider.Name)));
runCount++;
var data = new RetentionTimeProviderData(regressionType, retentionTimeProvider, standardPeptideList, heavyStandards);
if (data.RegressionSuccess ||
(ReferenceEquals(regressionType, IrtRegressionType.LINEAR) && data.CalcRegressionWith(retentionTimeProvider, standardPeptideList, items)))
{
AddRetentionTimesToDict(retentionTimeProvider, data.RegressionRefined, dictPeptideAverages, standardPeptideList);
}
providerData.Add(data);
monitor.UpdateProgress(status = status.ChangePercentComplete(runCount * 100 / providers.Length));
}
monitor.UpdateProgress(status.Complete());
return(new ProcessedIrtAverages(dictPeptideAverages, providerData));
}
