protected override void DoTest()
{
LibraryIonMobilityInfo driftInfoExplicitDT = null;
Testit(true, ref driftInfoExplicitDT); // Read both CCS and DT
if (_testCase == 1)
{
Testit(true, ref driftInfoExplicitDT); // Force conversion from CCS to DT, compare to previously read DT
Testit(false, ref driftInfoExplicitDT); // Compare our ability to locate drift peaks, and derive CCS from those, with explicitly provided values
}
// ReSharper restore ConditionIsAlwaysTrueOrFalse
}
private void Testit(
bool useDriftTimes, // If false, don't use any drift information in chromatogram extraction
ref LibraryIonMobilityInfo driftInfoExplicitDT
)
{
bool CCSonly = driftInfoExplicitDT != null; // If true, force conversion from CCS to DT
var ext = useDriftTimes ? (CCSonly ? "CCS" : "DT") : "train";
string skyfile = TestFilesDir.GetTestPath("test_" + ext + ".sky");
RunUI(() =>
{
SkylineWindow.NewDocument(true);
SkylineWindow.SaveDocument(skyfile);
});
Stopwatch loadStopwatch = new Stopwatch();
loadStopwatch.Start();
// Enable use of drift times in spectral library
var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
// ReSharper disable once ConditionIsAlwaysTrueOrFalse
peptideSettingsUI.IsUseSpectralLibraryDriftTimes = useDriftTimes;
peptideSettingsUI.SpectralLibraryDriftTimeResolvingPower = 50;
});
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
// Launch import peptide search wizard
var importPeptideSearchDlg = ShowDialog <ImportPeptideSearchDlg>(SkylineWindow.ShowImportPeptideSearchDlg);
var basename = _testCase == 1 ? "40minG_WBP_wide_z2-3_mid_BSA_5pmol_01" : "09_BSAtrypticdigest_5uL_IMQTOF_AltFramesdtramp_dAJS009";
var nextFile = _testCase == 1 ? null : "10_BSAtrypticdigest_5uL_IMQTOF_AltFramesdtramp_dAJS010.d";
var searchResults = GetTestPath(basename + ".pep.xml");
var doc = SkylineWindow.Document;
if (CCSonly || !useDriftTimes)
{
// Hide the drift time info provided by SpectrumMill, so we have to convert from CCS
var mzxmlFile = searchResults.Replace("pep.xml", "mzXML");
var fileContents = File.ReadAllText(mzxmlFile);
fileContents = fileContents.Replace(" DT=", " xx=");
if (!useDriftTimes)
{
fileContents = fileContents.Replace(" CCS=", " xxx=");
}
File.WriteAllText(mzxmlFile, fileContents);
}
var searchResultsList = new[] { searchResults };
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage ==
ImportPeptideSearchDlg.Pages.spectra_page);
importPeptideSearchDlg.BuildPepSearchLibControl.AddSearchFiles(searchResultsList);
importPeptideSearchDlg.BuildPepSearchLibControl.CutOffScore = 0.95;
importPeptideSearchDlg.BuildPepSearchLibControl.FilterForDocumentPeptides = false;
});
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()));
doc = WaitForDocumentChange(doc);
// Verify document library was built
string docLibPath = BiblioSpecLiteSpec.GetLibraryFileName(skyfile);
string redundantDocLibPath = BiblioSpecLiteSpec.GetRedundantName(docLibPath);
Assert.IsTrue(File.Exists(docLibPath) && File.Exists(redundantDocLibPath));
var librarySettings = SkylineWindow.Document.Settings.PeptideSettings.Libraries;
Assert.IsTrue(librarySettings.HasDocumentLibrary);
// We're on the "Extract Chromatograms" page of the wizard.
// All the files should be found, and we should
// just be able to move to the next page.
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page));
RunUI(() =>
{
var importResultsControl = (ImportResultsControl)importPeptideSearchDlg.ImportResultsControl;
importResultsControl.ExcludeSpectrumSourceFiles = true;
importResultsControl.UpdateResultsFiles(new [] { TestFilesDirs[0].PersistentFilesDir }, true); // Go look in the persistent files dir
});
if (searchResultsList.Length > 1)
{
// Deal with the common name start dialog
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importPeptideSearchDlg.ClickNextButtonNoCheck);
RunUI(() =>
{
importResultsNameDlg.NoDialog();
});
WaitForClosedForm(importResultsNameDlg);
}
else
{
RunUI(() => importPeptideSearchDlg.ClickNextButtonNoCheck());
}
// Modifications are already set up, so that page should get skipped.
RunUI(() => importPeptideSearchDlg.FullScanSettingsControl.PrecursorCharges = new [] { 2, 3, 4, 5 });
RunUI(() => importPeptideSearchDlg.FullScanSettingsControl.PrecursorMassAnalyzer = FullScanMassAnalyzerType.tof);
RunUI(() => importPeptideSearchDlg.ClickNextButton()); // Accept the full scan settings
// We're on the "Import FASTA" page of the wizard.
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.import_fasta_page);
importPeptideSearchDlg.ImportFastaControl.SetFastaContent(GetTestPath("SwissProt.bsa-mature"));
});
var peptidesPerProteinDlg = ShowDialog <PeptidesPerProteinDlg>(importPeptideSearchDlg.ClickNextButtonNoCheck);
OkDialog(peptidesPerProteinDlg, peptidesPerProteinDlg.OkDialog);
WaitForClosedForm(importPeptideSearchDlg);
var doc1 = WaitForDocumentChangeLoaded(doc, 15 * 60 * 1000); // 15 minutes
if (_testCase == 1)
{
AssertEx.IsDocumentState(doc1, null, 1, 34, 45, 135);
}
else
{
AssertEx.IsDocumentState(doc1, null, 1, 36, 43, 129);
}
loadStopwatch.Stop();
DebugLog.Info("load time = {0}", loadStopwatch.ElapsedMilliseconds);
var errmsg = "";
if (!useDriftTimes)
{
// Inspect the loaded data directly to derive DT and CCS
// 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.AddDriftTimePredictor);
RunUI(() =>
{
driftTimePredictorDlg.SetPredictorName("test");
driftTimePredictorDlg.SetResolvingPower(50);
driftTimePredictorDlg.GetDriftTimesFromResults();
driftTimePredictorDlg.OkDialog();
});
WaitForClosedForm(driftTimePredictorDlg);
RunUI(() =>
{
peptideSettingsDlg.OkDialog();
});
WaitForClosedForm(peptideSettingsDlg);
var document = SkylineWindow.Document;
var measuredDTs = document.Settings.PeptideSettings.Prediction.IonMobilityPredictor.MeasuredMobilityIons;
Assert.IsNotNull(driftInfoExplicitDT, "driftInfoExplicitDT != null");
var explicitDTs = driftInfoExplicitDT.GetIonMobilityDict();
string errMsgAll = string.Empty;
// A handful of peptides that really should have been trained on a clean sample
// CONSIDER: or are they multiple conformers? They have multiple hits with distinct IM in the pepXML
var expectedDiffs = LibKeyMap <double> .FromDictionary(new Dictionary <LibKey, double>
{
{ new PeptideLibraryKey("LC[+57.0]VLHEK", 2), 18.09 },
{ new PeptideLibraryKey("EC[+57.0]C[+57.0]DKPLLEK", 3), 7.0 },
{ new PeptideLibraryKey("SHC[+57.0]IAEVEK", 3), 6.0 },
{ new PeptideLibraryKey("DDPHAC[+57.0]YSTVFDK", 2), 24.0 }
}).AsDictionary();
foreach (var pair in doc1.PeptidePrecursorPairs)
{
string errMsg = string.Empty;
var key = new LibKey(pair.NodePep.ModifiedSequence, pair.NodeGroup.PrecursorAdduct);
double tolerCCS = 5;
if (expectedDiffs.ContainsKey(key))
{
tolerCCS = expectedDiffs[key] + .1;
}
if (!explicitDTs.ContainsKey(key))
{
errMsg += "Could not locate explicit IMS info for " + key + "\n";
}
var given = explicitDTs[key][0];
var measured = measuredDTs[key];
var msg = CheckDeltaPct(given.CollisionalCrossSectionSqA ?? 0, measured.CollisionalCrossSectionSqA ?? 0, tolerCCS, "measured CCS", key.ToString());
if (!string.IsNullOrEmpty(msg))
{
errMsg += msg + CheckDeltaPct(given.IonMobility.Mobility.Value, measured.IonMobility.Mobility.Value, -1, "measured drift time", key.ToString());
}
else
{
errMsg += CheckDelta(given.IonMobility.Mobility.Value, measured.IonMobility.Mobility.Value, 10.0, "measured drift time", key.ToString());
}
errMsg += CheckDelta(given.HighEnergyIonMobilityValueOffset, measured.HighEnergyIonMobilityValueOffset, 2.0, "measured drift time high energy offset", key.ToString());
if (!string.IsNullOrEmpty(errMsg))
{
errMsgAll += "\n" + errMsg;
}
}
if (!string.IsNullOrEmpty(errMsgAll))
{
Assert.Fail(errMsgAll);
}
return;
}
LibraryIonMobilityInfo libraryIonMobilityInfo;
doc1.Settings.PeptideSettings.Libraries.Libraries.First().TryGetIonMobilityInfos(doc1.MoleculeLibKeys.ToArray(), 0, out libraryIonMobilityInfo);
if (driftInfoExplicitDT == null)
{
driftInfoExplicitDT = libraryIonMobilityInfo;
}
else
{
var instrumentInfo = new DataFileInstrumentInfo(new MsDataFileImpl(GetTestPath(basename + ".d")));
var dictExplicitDT = driftInfoExplicitDT.GetIonMobilityDict();
foreach (var pep in doc1.Peptides)
{
foreach (var nodeGroup in pep.TransitionGroups)
{
double windowDT;
var calculatedDriftTime = doc1.Settings.GetIonMobility(
pep, nodeGroup, null, libraryIonMobilityInfo, instrumentInfo, 0, out windowDT);
var libKey = new LibKey(pep.ModifiedSequence, nodeGroup.PrecursorAdduct);
IonMobilityAndCCS[] infoValueExplicitDT;
if (!dictExplicitDT.TryGetValue(libKey, out infoValueExplicitDT))
{
errmsg += "No driftinfo value found for " + libKey + "\n";
}
else
{
var ionMobilityInfo = infoValueExplicitDT[0];
var delta = Math.Abs(ionMobilityInfo.IonMobility.Mobility.Value - calculatedDriftTime.IonMobility.Mobility.Value);
var acceptableDelta = (libKey.Sequence.StartsWith("DDPHAC") || libKey.Sequence.EndsWith("VLHEK")) ? 3: 1; // These were ambiguous matches
if (delta > acceptableDelta)
{
errmsg += String.Format("calculated DT ({0}) and explicit DT ({1}, CCS={4}) do not agree (abs delta = {2}) for {3}\n",
calculatedDriftTime.IonMobility, ionMobilityInfo.IonMobility,
delta, libKey,
ionMobilityInfo.CollisionalCrossSectionSqA ?? 0);
}
}
}
}
}
float tolerance = (float)doc1.Settings.TransitionSettings.Instrument.MzMatchTolerance;
double maxHeight = 0;
var results = doc1.Settings.MeasuredResults;
var numPeaks = _testCase == 1 ?
new[] { 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 10, 7, 10, 10, 10, 10, 8, 10, 10, 10, 10, 10, 10, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 10, 10, 8, 10, 10, 10, 10, 10 } :
new[] { 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10 };
int npIndex = 0;
foreach (var pair in doc1.PeptidePrecursorPairs)
{
ChromatogramGroupInfo[] chromGroupInfo;
Assert.IsTrue(results.TryLoadChromatogram(0, pair.NodePep, pair.NodeGroup,
tolerance, true, out chromGroupInfo));
foreach (var chromGroup in chromGroupInfo)
{
if (numPeaks[npIndex] != chromGroup.NumPeaks)
{
errmsg += String.Format("unexpected peak count {0} instead of {1} in chromatogram {2}\r\n", chromGroup.NumPeaks, numPeaks[npIndex], npIndex);
}
npIndex++;
foreach (var tranInfo in chromGroup.TransitionPointSets)
{
maxHeight = Math.Max(maxHeight, tranInfo.MaxIntensity);
}
}
}
Assert.IsTrue(errmsg.Length == 0, errmsg);
Assert.AreEqual(_testCase == 1 ? 2265204 : 1326442, maxHeight, 1);
// Does CCS show up in reports?
var expectedDtWindow = _testCase == 1 ? 0.74 : 0.94;
TestReports(doc1, 0, expectedDtWindow);
if (nextFile != null)
{
// Verify that we can use library generated for one file as the default for another without its own library
ImportResults(nextFile);
TestReports(SkylineWindow.Document, 1, expectedDtWindow);
}
// And verify roundtrip of ion mobility
AssertEx.RoundTrip(SkylineWindow.Document);
RunUI(() =>
{
SkylineWindow.SaveDocument(skyfile);
SkylineWindow.NewDocument(true);
SkylineWindow.OpenFile(skyfile);
});
TestReports(SkylineWindow.Document, 1, expectedDtWindow);
// Watch for problem with reimport after changed DT window
var docResolvingPower = SkylineWindow.Document;
var peptideSettingsUI2 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
// ReSharper disable once ConditionIsAlwaysTrueOrFalse
peptideSettingsUI2.IsUseSpectralLibraryDriftTimes = useDriftTimes;
peptideSettingsUI2.SpectralLibraryDriftTimeResolvingPower = 40;
});
OkDialog(peptideSettingsUI2, peptideSettingsUI2.OkDialog);
var docReimport = WaitForDocumentChangeLoaded(docResolvingPower);
// Reimport data for a replicate
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, dlg =>
{
var chromatograms = docReimport.Settings.MeasuredResults.Chromatograms;
dlg.SelectedChromatograms = new[] { chromatograms[0] };
dlg.ReimportResults();
dlg.OkDialog();
});
WaitForDocumentChangeLoaded(docReimport);
var expectedDtWindow0 = _testCase == 2 ? 1.175 : 0.92;
var expectedDtWindow1 = _testCase == 2 ? 0.94 : 0.92;
TestReports(SkylineWindow.Document, 0, expectedDtWindow0, string.Format(" row {0} case {1} ccsOnly {2}", 0, _testCase, CCSonly));
TestReports(SkylineWindow.Document, 1, expectedDtWindow1, string.Format(" row {0} case {1} ccsOnly {2}", 1, _testCase, CCSonly));
}
public override bool TryGetIonMobilities(int fileIndex, out LibraryIonMobilityInfo ionMobilities)
{
ionMobilities = null;
return(false);
}
public override bool TryGetIonMobilityInfos(LibKey[] targetIons, out LibraryIonMobilityInfo ionMobilities)
{
ionMobilities = null;
return(false);
}
public override bool TryGetIonMobilities(MsDataFileUri filePath, out LibraryIonMobilityInfo ionMobilities)
{
ionMobilities = null;
return(false);
}
/// <summary>
/// Made public for testing purposes only: exercises library and predictor but doesn't handle explicitly set drift times.
/// Use GetDriftTime() instead.
/// </summary>
public DriftTimeInfo GetDriftTimeHelper(LibKey chargedPeptide,
LibraryIonMobilityInfo libraryIonMobilityInfo, out double windowDtMsec)
{
if (DriftTimePredictor != null)
{
var result = DriftTimePredictor.GetDriftTimeInfo(chargedPeptide, out windowDtMsec);
if (result != null && result.DriftTimeMsec(false).HasValue)
return result;
}
if (libraryIonMobilityInfo != null)
{
var dt = libraryIonMobilityInfo.GetLibraryMeasuredDriftTimeAndHighEnergyOffset(chargedPeptide);
if ((dt != null) && dt.DriftTimeMsec(false).HasValue && (LibraryDriftTimesResolvingPower ?? 0) > 0)
{
windowDtMsec = 2.0 * dt.DriftTimeMsec(false).Value / LibraryDriftTimesResolvingPower.Value;
return dt;
}
}
windowDtMsec = 0;
return new DriftTimeInfo(null, 0);
}
/// <summary>
/// Get drift time for the charged peptide from explicitly set values, or our drift time predictor, or,
/// failing that, from the provided spectral library if it has bare drift times.
/// If no drift info is available, returns a new zero'd out drift time info object.
/// </summary>
public DriftTimeInfo GetDriftTime(PeptideDocNode nodePep,
TransitionGroupDocNode nodeGroup,
LibraryIonMobilityInfo libraryIonMobilityInfo, out double windowDtMsec)
{
if (nodeGroup.ExplicitValues.DriftTimeMsec.HasValue)
{
// Use the explicitly specified value
var result = new DriftTimeInfo(nodeGroup.ExplicitValues.DriftTimeMsec,
nodeGroup.ExplicitValues.DriftTimeHighEnergyOffsetMsec ?? 0);
// Now get the resolving power
if (DriftTimePredictor != null)
{
windowDtMsec = DriftTimePredictor.InverseResolvingPowerTimesTwo*result.DriftTimeMsec(false).Value;
}
else if (LibraryDriftTimesResolvingPower.HasValue)
{
windowDtMsec = 2.0 * result.DriftTimeMsec(false).Value / LibraryDriftTimesResolvingPower.Value;
}
else
{
windowDtMsec = 0;
}
return result;
}
else
{
return GetDriftTimeHelper(
new LibKey(nodePep.RawTextId, nodeGroup.TransitionGroup.PrecursorCharge), libraryIonMobilityInfo,
out windowDtMsec);
}
}
/// <summary>
/// Get all ion mobilities associated with this filepath. Then look at all the others
/// and get any that don't appear in the inital set, setting them up to be averaged.
/// </summary>
public bool TryGetIonMobilities(MsDataFileUri filePath, out LibraryIonMobilityInfo ionMobilities)
{
Assume.IsTrue(IsLoaded);
foreach (Library lib in _libraries)
{
// Only one of the available libraries may claim ownership of the file
// in question.
if (lib != null && lib.TryGetIonMobilities(filePath, out ionMobilities))
{
// TODO - or HACK, IF YOU PREFER: something better than this:
// Look at all available sublibraries, use them to backfill
// any missing drift time info in this one
var ionMobilitiesList = new List<LibraryIonMobilityInfo>();
LibraryIonMobilityInfo ionMobilitiesOther;
int i = 0;
while (lib.TryGetIonMobilities(i++, out ionMobilitiesOther)) // Returns false when i> internal list length
{
ionMobilitiesList.Add(ionMobilitiesOther);
}
for (i = 0; i < ionMobilitiesList.Count; i++)
{
var thisDict = ionMobilitiesList[i].GetIonMobilityDict();
foreach (var im in thisDict) // For each entry this sublibrary
{
// If this key is not in the source file in question
if (!ionMobilities.GetIonMobilityDict().ContainsKey(im.Key))
{
// Aggregate with any others (averaging happens elsewhere)
var info = new List<IonMobilityInfo>();
for (int j = i; j < ionMobilitiesList.Count; j++)
{
var thatDict = ionMobilitiesList[j].GetIonMobilityDict();
if (thatDict.ContainsKey(im.Key))
{
info.AddRange(thatDict[im.Key]);
}
}
if (info.Any())
{
ionMobilities.GetIonMobilityDict().Add(im.Key,info.ToArray());
}
}
}
}
return true;
}
}
ionMobilities = null;
return false;
}
public override bool TryGetIonMobilities(int fileIndex, out LibraryIonMobilityInfo ionMobilities)
{
ionMobilities = null;
return false;
}
public override bool TryGetIonMobilities(MsDataFileUri filePath, out LibraryIonMobilityInfo ionMobilities)
{
ionMobilities = null;
return false;
}
