public void TransitionLibraryDIAPrecursorExclusionTest()
{
// Create a document with the necessary library spectrum
LibraryManager libraryManager;
TestDocumentContainer docContainer;
int startRev;
SrmDocument document = LibrarySettingsTest.CreateNISTLibraryDocument(
">peptide1\nLECTDTLPDILENR",
true,
TEXT_LIB_YEAST_NIST_PRECURSOR,
out libraryManager,
out docContainer,
out startRev);
// Open up the transition filter settings and add a new isolation window scheme
List <IsolationWindow> isolationWindows = new List <IsolationWindow>();
// Parent mass is 844
isolationWindows.Add(new IsolationWindow(600, 700)); // simple windows
isolationWindows.Add(new IsolationWindow(700, 800)); // simple windows
isolationWindows.Add(new IsolationWindow(800, 900)); // simple windows
var settings = document.Settings
.ChangeTransitionLibraries(library =>
library.ChangePick(TransitionLibraryPick.all).
ChangeIonCount(10))
.ChangeTransitionFilter(filter =>
filter.ChangePeptideIonTypes(new[] { IonType.y, IonType.b })
.ChangeFragmentRangeFirstName("ion 1")
.ChangeFragmentRangeLastName("last ion")
.ChangeExclusionUseDIAWindow(true))
.ChangeTransitionFullScan(fs =>
fs.ChangeAcquisitionMethod(FullScanAcquisitionMethod.DIA,
new IsolationScheme("Test", isolationWindows)));
var docLibUnfiltered = document.ChangeSettings(settings);
Assert.AreEqual(10, docLibUnfiltered.PeptideTransitionCount);
Assert.AreEqual(1, docLibUnfiltered.PeptideTransitions.Count(nodeTran =>
nodeTran.Transition.Ordinal <4 || nodeTran.Transition.Ordinal> nodeTran.Transition.Group.Peptide.Sequence.Length - 4));
// Using a precursor filter should have no impact now, since the filter is being ignored
var settingsP = settings.ChangeTransitionFilter(filter =>
filter.ChangePrecursorMzWindow(TransitionFilter.MAX_EXCLUSION_WINDOW));
var docIgnorePrecursorMzWindow = docLibUnfiltered.ChangeSettings(settingsP);
Assert.AreSame(docLibUnfiltered.Children, docIgnorePrecursorMzWindow.Children);
// Should contain ions within the precursor window
const int countInWindow = 2;
const int countInOverlapWindow = 5;
Assert.AreEqual(countInWindow, docLibUnfiltered.PeptideTransitions.Count(nodeTran =>
nodeTran.Mz > 800 && nodeTran.Mz < 900));
Assert.AreEqual(countInOverlapWindow, docLibUnfiltered.PeptideTransitions.Count(nodeTran =>
nodeTran.Mz > 750 && nodeTran.Mz < 1250));
// Switch to filtered picking
settings = settings.ChangeTransitionLibraries(library => library.ChangePick(TransitionLibraryPick.filter));
var docLibFiltered = docLibUnfiltered.ChangeSettings(settings);
Assert.AreEqual(10, docLibFiltered.PeptideTransitionCount);
// Should not contain any more ions in the specified DIA window
Assert.AreEqual(0, docLibFiltered.PeptideTransitions.Count(nodeTran =>
nodeTran.Mz > 800 && nodeTran.Mz < 900));
// But should contain ions within the extended precursor window
const int countInOverlapWindowNew = 4;
Assert.AreEqual(countInOverlapWindowNew, docLibFiltered.PeptideTransitions.Count(nodeTran =>
nodeTran.Mz > 750 && nodeTran.Mz < 1250));
// But other transitions remain unchanged
Assert.AreEqual(docLibUnfiltered.PeptideTransitionCount - countInWindow,
docLibFiltered.PeptideTransitions.ToList().ConvertAll(nodeTran => nodeTran.Transition)
.Intersect(docLibUnfiltered.PeptideTransitions.ToList().ConvertAll(nodeTran => nodeTran.Transition)).Count());
// Add more windows to the document
isolationWindows.Add(new IsolationWindow(750, 850)); // overlapping windows
isolationWindows.Add(new IsolationWindow(840, 950)); // overlapping windows
isolationWindows.Add(new IsolationWindow(840, 1250)); // overlapping windows
var settingsNew = settings.ChangeTransitionFullScan(fs =>
fs.ChangeAcquisitionMethod(FullScanAcquisitionMethod.DIA,
new IsolationScheme("Test", isolationWindows)));
var docFilterAdditionalWindows = docLibFiltered.ChangeSettings(settingsNew);
// Check that now no more transitions are between 750 and 1250
Assert.AreEqual(10, docFilterAdditionalWindows.PeptideTransitionCount);
Assert.AreEqual(0, docFilterAdditionalWindows.PeptideTransitions.Count(nodeTran =>
nodeTran.Mz > 750 && nodeTran.Mz < 1250));
// But other transitions remain unchanged
Assert.AreEqual(docLibUnfiltered.PeptideTransitionCount - countInOverlapWindow,
docFilterAdditionalWindows.PeptideTransitions.ToList().ConvertAll(nodeTran => nodeTran.Transition)
.Intersect(docLibUnfiltered.PeptideTransitions.ToList().ConvertAll(nodeTran => nodeTran.Transition)).Count());
// Reset the settings, and make sure the transitions return to previous state
var docReset = docFilterAdditionalWindows.ChangeSettings(settings);
Assert.AreEqual(docLibFiltered, docReset);
// The filter should be turned off again when setting ExclusionUseDIAWindow to false
var settingsNoFilter = settings.ChangeTransitionFilter(filter =>
filter.ChangeExclusionUseDIAWindow(false));
var docNoFilterAgain = docLibFiltered.ChangeSettings(settingsNoFilter);
Assert.AreEqual(10, docNoFilterAgain.PeptideTransitionCount);
Assert.AreEqual(countInOverlapWindow, docNoFilterAgain.PeptideTransitions.Count(nodeTran =>
nodeTran.Mz > 750 && nodeTran.Mz < 1250));
}
public void TransitionLibrary07Test()
{
// Create a document with the necessary library spectrum
LibraryManager libraryManager;
TestDocumentContainer docContainer;
int startRev;
SrmDocument document = LibrarySettingsTest.CreateNISTLibraryDocument(
">peptide1\nLECTDTLPDILENR",
true,
TEXT_LIB_YEAST_NIST_PRECURSOR,
out libraryManager,
out docContainer,
out startRev);
// Open up the transition filter settings before testing the precursor m/z window
var settings = document.Settings
.ChangeTransitionLibraries(library =>
library.ChangePick(TransitionLibraryPick.all).
ChangeIonCount(10))
.ChangeTransitionFilter(filter =>
filter.ChangePeptideIonTypes(new[] { IonType.y, IonType.b })
.ChangeFragmentRangeFirstName("ion 4")
.ChangeFragmentRangeLastName("last ion - 3"));
var docLibUnfiltered = document.ChangeSettings(settings);
Assert.AreEqual(10, docLibUnfiltered.PeptideTransitionCount);
Assert.AreEqual(1, docLibUnfiltered.PeptideTransitions.Count(nodeTran =>
nodeTran.Transition.Ordinal <4 || nodeTran.Transition.Ordinal> nodeTran.Transition.Group.Peptide.Sequence.Length - 4));
// Using a precursor filter should have no impact now, since the filter is being ignored
var settingsP = settings.ChangeTransitionFilter(filter =>
filter.ChangePrecursorMzWindow(TransitionFilter.MAX_EXCLUSION_WINDOW));
var docIgnorePrecursorMzWindow = docLibUnfiltered.ChangeSettings(settingsP);
Assert.AreSame(docLibUnfiltered.Children, docIgnorePrecursorMzWindow.Children);
// Switch to filtered picking
settings = settings.ChangeTransitionLibraries(library => library.ChangePick(TransitionLibraryPick.filter));
var docLibFiltered = docLibUnfiltered.ChangeSettings(settings);
Assert.AreEqual(10, docLibFiltered.PeptideTransitionCount);
// Should have removed the ions outside the previously specified range
Assert.IsFalse(docLibFiltered.PeptideTransitions.Contains(nodeTran =>
nodeTran.Transition.Ordinal <4 || nodeTran.Transition.Ordinal> nodeTran.Transition.Group.Peptide.Sequence.Length - 4));
// But should contain ions within the precursor window
double precursorMz = docLibFiltered.PeptideTransitionGroups.ToArray()[0].PrecursorMz;
const int countInWindow = 2;
const double maxDelta = TransitionFilter.MAX_EXCLUSION_WINDOW / 2;
Assert.AreEqual(countInWindow, docLibFiltered.PeptideTransitions.Count(nodeTran =>
Math.Abs(precursorMz - nodeTran.Mz) < maxDelta));
// Set a precursor m/z window for real this time
settingsP = settings.ChangeTransitionFilter(filter =>
filter.ChangePrecursorMzWindow(TransitionFilter.MAX_EXCLUSION_WINDOW));
var docPrecursorMzWindow = docLibFiltered.ChangeSettings(settingsP);
Assert.AreEqual(10, docPrecursorMzWindow.PeptideTransitionCount);
// Make sure transitions in the window were removed
Assert.IsFalse(docPrecursorMzWindow.PeptideTransitions.Contains(nodeTran =>
Math.Abs(precursorMz - nodeTran.Mz) < maxDelta));
// But other transitions remain unchanged
Assert.AreEqual(docPrecursorMzWindow.PeptideTransitionCount - countInWindow,
docPrecursorMzWindow.PeptideTransitions.ToList().ConvertAll(nodeTran => nodeTran.Transition)
.Intersect(docLibFiltered.PeptideTransitions.ToList().ConvertAll(nodeTran => nodeTran.Transition)).Count());
// Reset the settings, and make sure the transitions return to previous state
var docReset = docPrecursorMzWindow.ChangeSettings(settings);
Assert.AreEqual(docLibFiltered, docReset);
// Restrict ion count chosen from the library
settings = settings.ChangeTransitionLibraries(library => library.ChangeIonCount(3))
.ChangeTransitionFilter(filter => filter.ChangePeptideIonTypes(new[] { IonType.y }));
var docThreeTran = docReset.ChangeSettings(settings);
Assert.AreEqual(3, docThreeTran.PeptideTransitionCount);
// Make sure ions below precursor m/z are present
Assert.AreEqual(2, docThreeTran.PeptideTransitions.Count(nodeTran => nodeTran.Mz < precursorMz));
// Change the filter and picking to library-plus-filter
// with a more restricted filter.
settings = settings
.ChangeTransitionLibraries(library =>
library.ChangePick(TransitionLibraryPick.all_plus))
.ChangeTransitionFilter(filter =>
filter.ChangeFragmentRangeFirstName("m/z > precursor")
.ChangeFragmentRangeLastName("3 ions"));
var docLibPlus = docThreeTran.ChangeSettings(settings);
Assert.AreEqual(5, docLibPlus.PeptideTransitionCount);
// Make sure ions below precursor m/z are present
Assert.AreEqual(3, docLibPlus.PeptideTransitions.Count(nodeTran => nodeTran.Mz > precursorMz));
}
