public DriftTimePredictor(string name,
IDictionary <LibKey, IonMobilityAndCCS> measuredMobilityIons,
IonMobilityWindowWidthCalculator.IonMobilityWindowWidthType windowWidthMode,
double resolvingPower,
double widthAtIonMobilityZero, double widthAtIonMobilityMax,
double fixedPeakWidth)
: base(name)
{
_windowWidthCalculator = new IonMobilityWindowWidthCalculator(windowWidthMode,
resolvingPower, widthAtIonMobilityZero, widthAtIonMobilityMax, fixedPeakWidth);
MeasuredMobilityIons = measuredMobilityIons;
Validate();
}
private static double driftTimeMax = 13.799765403988133; // Known max drift time for this file - use to mimic resolving power logic for test purposes
private static SrmDocument InitWatersImsMseDocument(TestFilesDir testFilesDir,
IonMobilityWindowWidthCalculator.IonMobilityWindowWidthType driftWindowWidthCalcType,
bool withDriftTimeFilter,
out string docPath)
{
var skyFile = "single_no_driftinfo.sky";
docPath = testFilesDir.GetTestPath(skyFile);
var cmdline = new CommandLine();
Assert.IsTrue(cmdline.OpenSkyFile(docPath)); // Handles any path shifts in database files
SrmDocument doc = cmdline.Document;
// Cause library load and subsequent document update
using (var docContainer = new ResultsTestDocumentContainer(null, docPath))
{
docContainer.SetDocument(doc, null, true);
docContainer.AssertComplete();
doc = docContainer.Document;
double resolvingPower = 100; // Test was originally written with resolving power 100
double widthAtDtMax = 2 * driftTimeMax / resolvingPower;
double fixedWidth = widthAtDtMax / 2;
var driftTimeWindowWidthCalculator = new IonMobilityWindowWidthCalculator(driftWindowWidthCalcType, resolvingPower, 0, widthAtDtMax, fixedWidth);
if (withDriftTimeFilter)
{
// Use the bare drift times in the spectral library
var librarySpec = new BiblioSpecLiteSpec("drift test",
testFilesDir.GetTestPath("waters-mobility.filtered-scaled.blib"));
doc = doc.ChangeSettings(
doc.Settings.ChangePeptideLibraries(lib => lib.ChangeLibrarySpecs(new[] { librarySpec })).
ChangeTransitionIonMobilityFiltering(p => p.ChangeFilterWindowWidthCalculator(driftTimeWindowWidthCalculator)).
ChangeTransitionIonMobilityFiltering(p => p.ChangeUseSpectralLibraryIonMobilityValues(true))
);
}
else
{
doc = doc.ChangeSettings(
doc.Settings.ChangeTransitionIonMobilityFiltering(im => im.ChangeFilterWindowWidthCalculator(driftTimeWindowWidthCalculator)));
}
}
return(doc);
}
private void WatersImsMseChromatogramTest(DriftFilterType mode,
IonMobilityWindowWidthCalculator.IonMobilityWindowWidthType driftWindowWidthCalcType,
RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules = RefinementSettings.ConvertToSmallMoleculesMode.none)
{
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none && !RunSmallMoleculeTestVersions)
{
Console.Write(MSG_SKIPPING_SMALLMOLECULE_TEST_VERSION);
return;
}
string subdir = (asSmallMolecules == RefinementSettings.ConvertToSmallMoleculesMode.none) ? null : asSmallMolecules.ToString();
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE, subdir);
bool withDriftTimeFilter = (mode != DriftFilterType.none); // Perform drift time filtering from blib file?
string docPath;
SrmDocument document = InitWatersImsMseDocument(testFilesDir, driftWindowWidthCalcType, withDriftTimeFilter, out docPath);
AssertEx.IsDocumentState(document, null, 1, 1, 1, 8); // Drift time lib load bumps the doc version, so does small mol conversion
var listChromatograms = new List <ChromatogramSet>();
// A small subset of the QC_HDMSE_02_UCA168_3495_082213 data set (RT 21.5-22.5) from Will Thompson
string mz5Path = "waters-mobility" + ExtensionTestContext.ExtMz5;
var testModeStr = withDriftTimeFilter ? "with drift times from spectral library" : "without drift time filtering";
listChromatograms.Add(AssertResult.FindChromatogramSet(document, new MsDataFilePath(mz5Path)) ??
new ChromatogramSet(Path.GetFileName(mz5Path).Replace('.', '_'), new[] { mz5Path }));
using (var docContainer = new ResultsTestDocumentContainer(document, docPath))
{
var doc = docContainer.Document;
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
AssertEx.IsTrue(docContainer.SetDocument(docResults, doc, true));
docContainer.AssertComplete();
document = docContainer.Document;
}
document = ConvertToSmallMolecules(document, ref docPath, new[] { mz5Path }, asSmallMolecules);
using (var docContainer = new ResultsTestDocumentContainer(document, docPath))
{
float tolerance = (float)document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
double maxHeight = 0;
var results = document.Settings.MeasuredResults;
AssertEx.AreEqual(1, document.MoleculePrecursorPairs.Count());
foreach (var pair in document.MoleculePrecursorPairs)
{
ChromatogramGroupInfo[] chromGroupInfo;
AssertEx.IsTrue(results.TryLoadChromatogram(0, pair.NodePep, pair.NodeGroup,
tolerance, true, out chromGroupInfo));
AssertEx.AreEqual(1, chromGroupInfo.Length, testModeStr + " chromGroupInfo.Length");
var chromGroup = chromGroupInfo[0];
int expectedPeaks;
if (withDriftTimeFilter)
{
expectedPeaks = 3;
}
else if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
expectedPeaks = 5;
}
else
{
expectedPeaks = 6; // No libraries
}
AssertEx.AreEqual(expectedPeaks, chromGroup.NumPeaks, testModeStr + " expectedPeaks"); // This will be higher if we don't filter on DT
foreach (var tranInfo in chromGroup.TransitionPointSets)
{
maxHeight = Math.Max(maxHeight, tranInfo.MaxIntensity);
}
}
var expectedFilteredMaxHeight =
driftWindowWidthCalcType == IonMobilityWindowWidthCalculator.IonMobilityWindowWidthType.fixed_width
? 5814
: 5226;
AssertEx.AreEqual(withDriftTimeFilter ? expectedFilteredMaxHeight : 20075, maxHeight, 1, testModeStr + " maxHeight"); // Without DT filtering, this will be much greater
// now drill down for specific values
int nPeptides = 0;
foreach (var nodePep in document.Molecules.Where(nodePep => !nodePep.Results[0].IsEmpty))
{
// expecting just one peptide result in this small data set
if (nodePep.Results[0].Sum(chromInfo => chromInfo.PeakCountRatio > 0 ? 1 : 0) > 0)
{
AssertEx.AreEqual(21.94865, (double)nodePep.GetMeasuredRetentionTime(0), .0001, testModeStr + " RT");
AssertEx.AreEqual(1.0, (double)nodePep.GetPeakCountRatio(0), 0.0001, testModeStr + "peak count ration");
nPeptides++;
}
}
AssertEx.AreEqual(1, nPeptides);
if (withDriftTimeFilter)
{
// Verify that the .imsdb or .blib file goes out in the share zipfile
for (int complete = 0; complete <= 1; complete++)
{
var sharePath =
testFilesDir.GetTestPath(complete == 1 ? "share_complete.zip" : "share_minimized.zip");
var share = new SrmDocumentSharing(document, docPath, sharePath,
new ShareType(complete == 1, SkylineVersion.CURRENT)); // Explicitly declaring version number forces a save before zip
share.Share(new SilentProgressMonitor());
var files = share.ListEntries().ToArray();
var imsdbFile = "waters-mobility.filtered-scaled.blib";
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none)
{
var ext = "." + imsdbFile.Split('.').Last();
imsdbFile = imsdbFile.Replace(ext, BiblioSpecLiteSpec.DotConvertedToSmallMolecules + ext);
}
AssertEx.IsTrue(files.Contains(imsdbFile));
// And round trip it to make sure we haven't left out any new features in minimized imsdb or blib files
share.Extract(new SilentProgressMonitor());
using (var cmdline = new CommandLine())
{
AssertEx.IsTrue(cmdline.OpenSkyFile(share.DocumentPath)); // Handles any path shifts in database files, like our .imsdb file
var document2 = cmdline.Document;
AssertEx.IsNotNull(document2);
AssertEx.IsTrue(docContainer.SetDocument(document2, docContainer.Document, true));
docContainer.AssertComplete();
document2 = docContainer.Document;
var im = document2.Settings.GetIonMobilities(document2.MoleculeLibKeys.ToArray(), new MsDataFilePath(mz5Path));
var pep = document2.Molecules.First();
var expectedWidth =
driftWindowWidthCalcType == IonMobilityWindowWidthCalculator.IonMobilityWindowWidthType.fixed_width
? 0.13799765403988132
: 0.077224865797235934;
foreach (TransitionGroupDocNode nodeGroup in pep.Children)
{
var centerDriftTime = document2.Settings.GetIonMobilityFilter(
pep, nodeGroup, null, im, null, driftTimeMax);
AssertEx.AreEqual(3.86124, centerDriftTime.IonMobilityAndCCS.IonMobility.Mobility.Value, .0001, testModeStr + " ccs");
AssertEx.AreEqual(expectedWidth, centerDriftTime.IonMobilityExtractionWindowWidth.Value, .0001, testModeStr + " dtWidth");
}
}
}
}
}
}