public static void SelectAndApplyPeak(string modifiedSequence, double?precursorMz, string resultsName, bool subsequent, double rt)
{
bool found = false;
var skylineWindow = Program.MainWindow;
var doc = skylineWindow.Document;
IdentityPath identityPath = null;
var libKeyToMatch = new PeptideLibraryKey(modifiedSequence, 0);
foreach (PeptideGroupDocNode nodePepGroup in doc.MoleculeGroups)
{
foreach (var nodePep in nodePepGroup.Peptides.Where(nodePep => LibKeyIndex.KeysMatch(libKeyToMatch, nodePep.ModifiedTarget.GetLibKey(Adduct.EMPTY))))
{
var nodeTranGroup = precursorMz.HasValue
? nodePep.TransitionGroups.First(tranGroup => Math.Abs(tranGroup.PrecursorMz - precursorMz.Value) < 0.01)
: nodePep.TransitionGroups.First();
identityPath = new IdentityPath(nodePepGroup.Id, nodePep.Id, nodeTranGroup.Id);
IdentityPath path = identityPath;
skylineWindow.SelectedPath = path;
found = true;
break;
}
if (found)
{
break;
}
}
if (!found)
{
Assert.Fail("Could not find peptide {0}", modifiedSequence);
}
found = false;
var chromatograms = doc.Settings.MeasuredResults.Chromatograms;
foreach (var chromatogram in chromatograms.Where(chromSet => chromSet.Name.Equals(resultsName)))
{
found = true;
ChromatogramSet chromSet = chromatogram;
skylineWindow.SelectedResultsIndex = chromatograms.IndexOf(chromSet);
skylineWindow.ModifyDocument("change peak", document =>
document.ChangePeak(identityPath, chromSet.Name, chromSet.MSDataFilePaths.First(), null, rt, UserSet.TRUE));
break;
}
if (!found)
{
Assert.Fail("Could not find results {0}", resultsName);
}
skylineWindow.ApplyPeak(subsequent);
}
public IEnumerable <DbSpectrum> GetSpectraByPeptide(MsDataFileUri file, LibKey libKey)
{
foreach (var spectrum in GetSpectraByFile(file))
{
if (string.IsNullOrWhiteSpace(spectrum.DocumentPeptide))
{
continue;
}
var key = new PeptideLibraryKey(spectrum.DocumentPeptide,
spectrum.DocumentPrecursorCharge.GetValueOrDefault());
if (LibKeyIndex.KeysMatch(libKey.LibraryKey, key))
{
yield return(spectrum);
}
}
}
protected override bool IsMatch(Target seqMod, PeptideDocNode nodePepMod, out TransitionGroupDocNode nodeGroup)
{
foreach (TransitionGroupDocNode nodeGroupChild in nodePepMod.Children)
{
nodeGroup = nodeGroupChild;
var calc = Settings.TryGetPrecursorCalc(nodeGroupChild.TransitionGroup.LabelType, nodePepMod.ExplicitMods);
if (calc == null)
{
return(false);
}
var modSequence = calc.GetModifiedSequence(nodePepMod.Peptide.Target, false);
// If this sequence matches the sequence of the library peptide, a match has been found.
if (LibKeyIndex.KeysMatch(seqMod.GetLibKey(Adduct.EMPTY), modSequence.GetLibKey(Adduct.EMPTY)))
{
return(true);
}
}
nodeGroup = null;
return(false);
}
protected override void DoTest()
{
string skyFile = TestFilesDir.GetTestPath("test_measured_drift_times_perf.sky");
Program.ExtraRawFileSearchFolder = TestFilesDir.PersistentFilesDir; // So we don't have to reload the raw files, which have moved relative to skyd file
RunUI(() => SkylineWindow.OpenFile(skyFile));
var document = WaitForDocumentLoaded(240000); // If it decides to remake chromatograms this can take awhile
AssertEx.IsDocumentState(document, null, 1, 34, 38, 398);
RunUI(() =>
{
SkylineWindow.SaveDocument(TestFilesDir.GetTestPath("local.sky")); // Avoid "document changed since last edit" message
document = SkylineWindow.DocumentUI;
});
var curatedDTs = document.Settings.PeptideSettings.Prediction.IonMobilityPredictor.MeasuredMobilityIons;
var measuredDTs = new List <IDictionary <LibKey, IonMobilityAndCCS> >();
var precursors = new LibKeyIndex(document.MoleculePrecursorPairs.Select(
p => p.NodePep.ModifiedTarget.GetLibKey(p.NodeGroup.PrecursorAdduct).LibraryKey));
for (var pass = 0; pass < 2; pass++)
{
// Verify ability to extract predictions from raw data
var peptideSettingsDlg = ShowDialog <PeptideSettingsUI>(
() => SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Prediction));
// Simulate user picking Edit Current from the Drift Time Predictor combo control
var driftTimePredictorDlg = ShowDialog <EditDriftTimePredictorDlg>(peptideSettingsDlg.EditDriftTimePredictor);
RunUI(() =>
{
driftTimePredictorDlg.SetOffsetHighEnergySpectraCheckbox(true);
driftTimePredictorDlg.GetDriftTimesFromResults();
driftTimePredictorDlg.OkDialog(true); // Force overwrite if a named predictor already exists
});
WaitForClosedForm(driftTimePredictorDlg);
RunUI(() =>
{
peptideSettingsDlg.OkDialog();
});
WaitForClosedForm(peptideSettingsDlg);
document = SkylineWindow.Document;
measuredDTs.Add(document.Settings.PeptideSettings.Prediction.IonMobilityPredictor.MeasuredMobilityIons);
var count = 0;
foreach (var key in curatedDTs.Keys)
{
if (precursors.ItemsMatching(key.LibraryKey, true).Any())
{
count++;
Assert.AreNotEqual(curatedDTs[key].IonMobility.Mobility, measuredDTs[pass][key].IonMobility.Mobility, "measured drift time should differ somewhat for " + key);
}
Assert.AreEqual(curatedDTs[key].IonMobility.Mobility.Value, measuredDTs[pass][key].IonMobility.Mobility.Value, 1.0, "measured drift time differs too much for " + key);
Assert.AreEqual(curatedDTs[key].HighEnergyIonMobilityValueOffset, measuredDTs[pass][key].HighEnergyIonMobilityValueOffset, 2.0, "measured drift time high energy offset differs too much for " + key);
}
Assert.AreEqual(document.MoleculeTransitionGroupCount, count, "did not find drift times for all precursors"); // Expect to find a value for each precursor
if (pass == 1)
{
break;
}
// Verify that we select based on strongest results by removing the training set and relying on the other noisier set
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, dlg =>
{
var chromatograms = document.Settings.MeasuredResults.Chromatograms;
var chromTraining = chromatograms[0];
var chroms = new[] { chromTraining };
dlg.SelectedChromatograms = chroms; // Passing this chromatograms[0] results in the other set being deleted - compiler problem?
dlg.RemoveReplicates();
dlg.OkDialog();
});
document = WaitForDocumentChange(document);
Assert.AreEqual(1, document.Settings.MeasuredResults.Chromatograms.Count);
}
// Results should be slightly different without the training set of chromatograms to contain a potentially stronger peak
var ccount = 0;
var noChange = new List <LibKey>();
foreach (var key in measuredDTs[0].Keys)
{
if (precursors.ItemsMatching(key, true).Any())
{
ccount++;
if (measuredDTs[0][key].GetHighEnergyDriftTimeMsec().Value == measuredDTs[1][key].GetHighEnergyDriftTimeMsec().Value)
{
noChange.Add(key);
}
}
Assert.AreEqual(measuredDTs[0][key].IonMobility.Mobility.Value, measuredDTs[1][key].IonMobility.Mobility.Value, 1.0, "averaged measured drift time differs for " + key);
Assert.AreEqual(measuredDTs[0][key].HighEnergyIonMobilityValueOffset, measuredDTs[1][key].HighEnergyIonMobilityValueOffset, 2.0, "averaged measured drift time high energy offset differs for " + key);
Assert.AreEqual(measuredDTs[0][key].CollisionalCrossSectionSqA.Value, measuredDTs[1][key].CollisionalCrossSectionSqA.Value, 1.0, "averaged measured CCS differs for " + key);
}
Assert.AreEqual(document.MoleculeTransitionGroupCount, ccount, "did not find drift times for all precursors"); // Expect to find a value for each precursor
Assert.IsTrue(noChange.Count < ccount / 2, "expected most values to shift a little without the nice clean training data");
// And finally verify ability to reimport with altered drift filter (would formerly fail on an erroneous Assume)
// Simulate user picking Edit Current from the Drift Time Predictor combo control, and messing with all the measured drift time values
var peptideSettingsDlg2 = ShowDialog <PeptideSettingsUI>(
() => SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Prediction));
var driftTimePredictorDlg2 = ShowDialog <EditDriftTimePredictorDlg>(peptideSettingsDlg2.EditDriftTimePredictor);
RunUI(() =>
{
var oldPredictor = driftTimePredictorDlg2.Predictor;
var dict = new Dictionary <LibKey, IonMobilityAndCCS>();
foreach (var entry in oldPredictor.MeasuredMobilityIons)
{
dict.Add(entry.Key, entry.Value.ChangeIonMobilityValue(entry.Value.IonMobility.ChangeIonMobility(entry.Value.IonMobility.Mobility ?? 0 + .5)));
}
driftTimePredictorDlg2.Predictor = oldPredictor.ChangeMeasuredMobilityIons(dict).ChangeName("test") as IonMobilityPredictor;
driftTimePredictorDlg2.OkDialog(true); // Force overwrite if a named predictor already exists
});
WaitForClosedForm(driftTimePredictorDlg2);
RunUI(() =>
{
peptideSettingsDlg2.OkDialog();
});
WaitForClosedForm(peptideSettingsDlg2);
var docChangedDriftTimePredictor = WaitForDocumentChange(document);
// Reimport data for a replicate - without the fix this will throw
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, dlg =>
{
var chromatograms = docChangedDriftTimePredictor.Settings.MeasuredResults.Chromatograms;
dlg.SelectedChromatograms = new[] { chromatograms[0] };
dlg.ReimportResults();
dlg.OkDialog();
});
WaitForDocumentChangeLoaded(docChangedDriftTimePredictor, WAIT_TIME * 2);
}
public static OptimizationDb ConvertFromOldFormat(string path, IProgressMonitor loadMonitor, ProgressStatus status, SrmDocument document)
{
// Try to open assuming old format (Id, PeptideModSeq, Charge, Mz, Value, Type)
var precursors = new Dictionary <Target, HashSet <int> >(); // PeptideModSeq -> charges
var optimizations = new List <Tuple <DbOptimization, double> >(); // DbOptimization, product m/z
int maxCharge = 1;
using (SQLiteConnection connection = new SQLiteConnection(@"Data Source = " + path))
using (SQLiteCommand command = new SQLiteCommand(connection))
{
connection.Open();
command.CommandText = @"SELECT PeptideModSeq, Charge, Mz, Value, Type FROM OptimizationLibrary";
using (SQLiteDataReader reader = command.ExecuteReader())
{
while (reader.Read())
{
var type = (OptimizationType)reader[@"Type"];
var modifiedSequence = new Target(reader[@"PeptideModSeq"].ToString());
var charge = (int)reader[@"Charge"];
var productMz = (double)reader[@"Mz"];
var value = (double)reader[@"Value"];
optimizations.Add(new Tuple <DbOptimization, double>(new DbOptimization(type, modifiedSequence, Adduct.FromChargeProtonated(charge), string.Empty, Adduct.EMPTY, value), productMz));
if (!precursors.ContainsKey(modifiedSequence))
{
precursors[modifiedSequence] = new HashSet <int>();
}
precursors[modifiedSequence].Add(charge);
if (charge > maxCharge)
{
maxCharge = charge;
}
}
}
}
var peptideList = (from precursor in precursors
from charge in precursor.Value
select string.Format(@"{0}{1}", precursor.Key, Transition.GetChargeIndicator(Adduct.FromChargeProtonated(charge)))
).ToList();
var newDoc = new SrmDocument(document != null ? document.Settings : SrmSettingsList.GetDefault());
newDoc = newDoc.ChangeSettings(newDoc.Settings
.ChangePeptideLibraries(libs => libs.ChangePick(PeptidePick.filter))
.ChangeTransitionFilter(filter =>
filter.ChangeFragmentRangeFirstName(@"ion 1")
.ChangeFragmentRangeLastName(@"last ion")
.ChangePeptideProductCharges(Enumerable.Range(1, maxCharge).Select(Adduct.FromChargeProtonated).ToList()) // TODO(bspratt) negative charge peptides
.ChangePeptideIonTypes(new [] { IonType.y, IonType.b })) // TODO(bspratt) generalize to molecules?
.ChangeTransitionLibraries(libs => libs.ChangePick(TransitionLibraryPick.none))
);
var matcher = new ModificationMatcher();
matcher.CreateMatches(newDoc.Settings, peptideList, Settings.Default.StaticModList, Settings.Default.HeavyModList);
FastaImporter importer = new FastaImporter(newDoc, matcher);
// ReSharper disable LocalizableElement
string text = string.Format(">>{0}\r\n{1}", newDoc.GetPeptideGroupId(true), TextUtil.LineSeparate(peptideList));
// ReSharper restore LocalizableElement
PeptideGroupDocNode imported = importer.Import(new StringReader(text), null, Helpers.CountLinesInString(text)).First();
int optimizationsUpdated = 0;
foreach (PeptideDocNode nodePep in imported.Children)
{
foreach (var nodeGroup in nodePep.TransitionGroups)
{
var charge = nodeGroup.PrecursorAdduct;
var libKeyToMatch = newDoc.Settings.GetSourceTarget(nodePep).GetLibKey(charge).LibraryKey;
foreach (var nodeTran in nodeGroup.Transitions)
{
double productMz = nodeTran.Mz;
foreach (var optimization in optimizations.Where(opt =>
string.IsNullOrEmpty(opt.Item1.FragmentIon) &&
opt.Item1.ProductAdduct.IsEmpty &&
Math.Abs(opt.Item2 - productMz) < 0.00001))
{
var optLibKey = optimization.Item1.Target.GetLibKey(optimization.Item1.Adduct).LibraryKey;
if (!LibKeyIndex.KeysMatch(optLibKey, libKeyToMatch))
{
continue;
}
optimization.Item1.FragmentIon = nodeTran.FragmentIonName;
optimization.Item1.ProductAdduct = nodeTran.Transition.Adduct;
++optimizationsUpdated;
}
}
}
}
if (optimizations.Count > optimizationsUpdated)
{
throw new OptimizationsOpeningException(string.Format(Resources.OptimizationDb_ConvertFromOldFormat_Failed_to_convert__0__optimizations_to_new_format_,
optimizations.Count - optimizationsUpdated));
}
using (var fs = new FileSaver(path))
{
OptimizationDb db = CreateOptimizationDb(fs.SafeName);
db.UpdateOptimizations(optimizations.Select(opt => opt.Item1).ToArray(), new DbOptimization[0]);
fs.Commit();
if (loadMonitor != null)
{
loadMonitor.UpdateProgress(status.ChangePercentComplete(100));
}
return(GetOptimizationDb(fs.RealName, null, null));
}
}
protected override void DoTest()
{
// IsPauseForScreenShots = true; // For a quick demo when you need it
string skyFile = TestFilesDir.GetTestPath("test_measured_drift_times_perf.sky");
Program.ExtraRawFileSearchFolder = TestFilesDir.PersistentFilesDir; // So we don't have to reload the raw files, which have moved relative to skyd file
RunUI(() => SkylineWindow.OpenFile(skyFile));
var document = WaitForDocumentLoaded(240000); // If it decides to remake chromatograms this can take awhile
AssertEx.IsDocumentState(document, null, 1, 34, 38, 398);
RunUI(() =>
{
SkylineWindow.SaveDocument(TestFilesDir.GetTestPath("local.sky")); // Avoid "document changed since last edit" message
document = SkylineWindow.DocumentUI;
});
List <ValidatingIonMobilityPrecursor> curatedDTs = null;
var measuredDTs = new List <List <ValidatingIonMobilityPrecursor> >();
var precursors = new LibKeyIndex(document.MoleculePrecursorPairs.Select(
p => p.NodePep.ModifiedTarget.GetLibKey(p.NodeGroup.PrecursorAdduct).LibraryKey));
PauseForScreenShot(@"Legacy ion mobility values loaded, placed in .imsdb database file"); // For a quick demo when you need it
for (var pass = 0; pass < 2; pass++)
{
// Verify ability to extract predictions from raw data
var transitionSettingsDlg = ShowDialog <TransitionSettingsUI>(
() => SkylineWindow.ShowTransitionSettingsUI(TransitionSettingsUI.TABS.IonMobility));
PauseForScreenShot("new Transition Settings tab"); // For a quick demo when you need it
// Simulate user picking Edit Current from the Ion Mobility Library combo control
var ionMobilityLibraryDlg = ShowDialog <EditIonMobilityLibraryDlg>(transitionSettingsDlg.IonMobilityControl.EditIonMobilityLibrary);
PauseForScreenShot("next, we'll update values with 'Use Results' button"); // For a quick demo when you need it
RunUI(() =>
{
if (curatedDTs == null)
{
curatedDTs = ionMobilityLibraryDlg.LibraryMobilitiesFlat.ToList();
}
ionMobilityLibraryDlg.SetOffsetHighEnergySpectraCheckbox(true);
ionMobilityLibraryDlg.GetIonMobilitiesFromResults();
});
PauseForScreenShot("values updated");// For a quick demo when you need it
RunUI(() =>
{
measuredDTs.Add(ionMobilityLibraryDlg.LibraryMobilitiesFlat.ToList());
ionMobilityLibraryDlg.OkDialog();
});
WaitForClosedForm(ionMobilityLibraryDlg);
RunUI(() =>
{
transitionSettingsDlg.OkDialog();
});
WaitForClosedForm(transitionSettingsDlg);
document = SkylineWindow.Document;
var count = 0;
for (var n = 0; n < curatedDTs.Count; n++)
{
var cdt = curatedDTs[n];
var key = cdt.Precursor;
var indexM = measuredDTs[pass].FindIndex(m => m.Precursor.Equals(key));
var measured = measuredDTs[pass][indexM];
var measuredDT = measured.IonMobility;
var measuredHEO = measured.HighEnergyIonMobilityOffset;
if (precursors.ItemsMatching(key, true).Any())
{
count++;
AssertEx.AreNotEqual(cdt.IonMobility, measuredDT, "measured drift time should differ somewhat for " + measured.Precursor);
}
AssertEx.AreEqual(cdt.IonMobility, measuredDT, 1.0, "measured drift time differs too much for " + key);
AssertEx.AreEqual(cdt.HighEnergyIonMobilityOffset, measuredHEO, 2.0, "measured drift time high energy offset differs too much for " + key);
}
AssertEx.AreEqual(document.MoleculeTransitionGroupCount, count, "did not find drift times for all precursors"); // Expect to find a value for each precursor
if (pass == 1)
{
break;
}
// Verify that we select based on strongest results by removing the training set and relying on the other noisier set
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, dlg =>
{
var chromatograms = document.Settings.MeasuredResults.Chromatograms;
var chromTraining = chromatograms[0];
var chroms = new[] { chromTraining };
dlg.SelectedChromatograms = chroms; // Passing this chromatograms[0] results in the other set being deleted - compiler problem?
dlg.RemoveReplicates();
dlg.OkDialog();
});
document = WaitForDocumentChange(document);
AssertEx.AreEqual(1, document.Settings.MeasuredResults.Chromatograms.Count);
}
// Results should be slightly different without the training set of chromatograms to contain a potentially stronger peak
var ccount = 0;
var noChange = new List <LibKey>();
for (var n = 0; n < measuredDTs[0].Count; n++)
{
var validatingIonMobilityPeptide0 = measuredDTs[0][n];
var validatingIonMobilityPeptide1 = measuredDTs[1][n];
var key = measuredDTs[0][n].Precursor;
if (precursors.ItemsMatching(key, true).Any())
{
ccount++;
if (validatingIonMobilityPeptide0.HighEnergyIonMobilityOffset == validatingIonMobilityPeptide1.HighEnergyIonMobilityOffset)
{
noChange.Add(key);
}
}
AssertEx.AreEqual(validatingIonMobilityPeptide0.IonMobility, validatingIonMobilityPeptide1.IonMobility, 1.0, "averaged measured drift time differs for " + key);
AssertEx.AreEqual(validatingIonMobilityPeptide0.HighEnergyIonMobilityOffset, validatingIonMobilityPeptide1.HighEnergyIonMobilityOffset, 2.0, "averaged measured drift time high energy offset differs for " + key);
AssertEx.AreEqual(validatingIonMobilityPeptide0.CollisionalCrossSectionSqA, validatingIonMobilityPeptide1.CollisionalCrossSectionSqA, 1.0, "averaged measured CCS differs for " + key);
}
AssertEx.AreEqual(document.MoleculeTransitionGroupCount, ccount, "did not find drift times for all precursors"); // Expect to find a value for each precursor
AssertEx.IsTrue(noChange.Count < ccount / 2, "expected most values to shift a little without the nice clean training data");
// And finally verify ability to reimport with altered drift filter (would formerly fail on an erroneous Assume)
// Simulate user picking Edit Current from the Ion Mobility Library combo control, and messing with all the measured drift time values
var transitionSettingsDlg2 = ShowDialog <TransitionSettingsUI>(
() => SkylineWindow.ShowTransitionSettingsUI(TransitionSettingsUI.TABS.Prediction));
var editIonMobilityLibraryDlg = ShowDialog <EditIonMobilityLibraryDlg>(transitionSettingsDlg2.IonMobilityControl.EditIonMobilityLibrary);
RunUI(() =>
{
var revised = new List <ValidatingIonMobilityPrecursor>();
foreach (var item in editIonMobilityLibraryDlg.LibraryMobilitiesFlat)
{
var im = item.IonMobility;
var heo = item.HighEnergyIonMobilityOffset;
revised.Add(new ValidatingIonMobilityPrecursor(item.Precursor,
IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.GetIonMobilityValue(im * 1.02, item.IonMobilityUnits),
item.CollisionalCrossSectionSqA * 1.02, heo * 1.02)));
}
editIonMobilityLibraryDlg.LibraryMobilitiesFlat = revised;
editIonMobilityLibraryDlg.OkDialog();
});
WaitForClosedForm(editIonMobilityLibraryDlg);
RunUI(() =>
{
transitionSettingsDlg2.OkDialog();
});
WaitForClosedForm(transitionSettingsDlg2);
var docChangedDriftTimePredictor = WaitForDocumentChange(document);
// Reimport data for a replicate - without the fix this will throw
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, dlg =>
{
var chromatograms = docChangedDriftTimePredictor.Settings.MeasuredResults.Chromatograms;
dlg.SelectedChromatograms = new[] { chromatograms[0] };
dlg.ReimportResults();
dlg.OkDialog();
});
WaitForDocumentChangeLoaded(docChangedDriftTimePredictor, WAIT_TIME * 2);
}
