public void RefineDocumentTest()
{
TestFilesDir testFilesDir = new TestFilesDir(TestContext, @"TestA\Refine.zip");
var document = InitRefineDocument(testFilesDir);
AssertEx.Serializable(document); // This checks a longstanding schema error
// First check a few refinements which should not change the document
var refineSettings = new RefinementSettings();
Assert.AreSame(document, refineSettings.Refine(document));
refineSettings.MinPeptidesPerProtein = (TestSmallMolecules ? 1 : 3); // That magic small molecule node has just one child
Assert.AreSame(document, refineSettings.Refine(document));
refineSettings.MinTransitionsPepPrecursor = (TestSmallMolecules ? 1 : 2);
Assert.AreSame(document, refineSettings.Refine(document));
// Remove the protein with only 3 peptides
refineSettings.MinPeptidesPerProtein = 4;
Assert.AreEqual(document.PeptideGroupCount - 1, refineSettings.Refine(document).PeptideGroupCount);
refineSettings.MinPeptidesPerProtein = 1;
// Remove the precursor with only 2 transitions
refineSettings.MinTransitionsPepPrecursor = 3;
Assert.AreEqual(document.PeptideTransitionGroupCount - 1, refineSettings.Refine(document).PeptideTransitionGroupCount);
refineSettings.MinTransitionsPepPrecursor = null;
// Remove the heavy precursor
refineSettings.RefineLabelType = IsotopeLabelType.heavy;
Assert.AreEqual(document.PeptideTransitionGroupCount - 1, refineSettings.Refine(document).PeptideTransitionGroupCount);
// Remove everything but the heavy precursor
refineSettings.RefineLabelType = IsotopeLabelType.light;
var docRefined = refineSettings.Refine(document);
AssertEx.IsDocumentState(docRefined, 1, 1, 1, 1, 4);
// Perform the operation again without protein removal
refineSettings.MinPeptidesPerProtein = null;
docRefined = refineSettings.Refine(document);
AssertEx.IsDocumentState(docRefined, 1, 4, 1, 1, 4);
refineSettings.RefineLabelType = null;
// Remove repeated peptides
refineSettings.RemoveRepeatedPeptides = true;
Assert.AreEqual(document.PeptideCount - 2, refineSettings.Refine(document).PeptideCount);
// Remove duplicate peptides
refineSettings.RemoveDuplicatePeptides = true;
Assert.AreEqual(document.PeptideCount - 3, refineSettings.Refine(document).PeptideCount);
// Try settings that remove everything from the document
refineSettings = new RefinementSettings {
MinPeptidesPerProtein = 20
};
Assert.AreEqual(0, refineSettings.Refine(document).PeptideGroupCount);
refineSettings.MinPeptidesPerProtein = 1;
refineSettings.MinTransitionsPepPrecursor = 20;
Assert.AreEqual(0, refineSettings.Refine(document).PeptideGroupCount);
testFilesDir.Dispose();
}
public void RefineDocumentTest()
{
var document = InitRefineDocument(RefinementSettings.ConvertToSmallMoleculesMode.none);
// First check a few refinements which should not change the document
var refineSettings = new RefinementSettings();
Assert.AreSame(document, refineSettings.Refine(document));
refineSettings.MinPeptidesPerProtein = 3;
Assert.AreSame(document, refineSettings.Refine(document));
refineSettings.MinTransitionsPepPrecursor = 2;
Assert.AreSame(document, refineSettings.Refine(document));
// Remove the protein with only 3 peptides
refineSettings.MinPeptidesPerProtein = 4;
Assert.AreEqual(document.PeptideGroupCount - 1, refineSettings.Refine(document).PeptideGroupCount);
refineSettings.MinPeptidesPerProtein = 1;
// Remove the precursor with only 2 transitions
refineSettings.MinTransitionsPepPrecursor = 3;
Assert.AreEqual(document.PeptideTransitionGroupCount - 1, refineSettings.Refine(document).PeptideTransitionGroupCount);
refineSettings.MinTransitionsPepPrecursor = null;
// Remove the heavy precursor
refineSettings.RefineLabelType = IsotopeLabelType.heavy;
Assert.AreEqual(document.PeptideTransitionGroupCount - 1, refineSettings.Refine(document).PeptideTransitionGroupCount);
// Remove everything but the heavy precursor
refineSettings.RefineLabelType = IsotopeLabelType.light;
var docRefined = refineSettings.Refine(document);
AssertEx.IsDocumentState(docRefined, null, 1, 1, 1, 4);
// Perform the operation again without protein removal
refineSettings.MinPeptidesPerProtein = null;
docRefined = refineSettings.Refine(document);
AssertEx.IsDocumentState(docRefined, null, 4, 1, 1, 4);
refineSettings.RefineLabelType = null;
// Remove repeated peptides
refineSettings.RemoveRepeatedPeptides = true;
Assert.AreEqual(document.PeptideCount - 2, refineSettings.Refine(document).PeptideCount);
// Remove duplicate peptides
refineSettings.RemoveDuplicatePeptides = true;
Assert.AreEqual(document.PeptideCount - 3, refineSettings.Refine(document).PeptideCount);
// Try settings that remove everything from the document
refineSettings = new RefinementSettings {
MinPeptidesPerProtein = 20
};
Assert.AreEqual(0, refineSettings.Refine(document).PeptideGroupCount);
refineSettings.MinPeptidesPerProtein = 1;
refineSettings.MinTransitionsPepPrecursor = 20;
Assert.AreEqual(0, refineSettings.Refine(document).PeptideGroupCount);
}
public static SrmDocument ChangeAutoManageChildren(SrmDocument document, PickLevel which, bool autoPick)
{
var refine = new RefinementSettings {
AutoPickChildrenAll = which, AutoPickChildrenOff = !autoPick
};
return(refine.Refine(document));
}
public void RemoveDuplicatePeptidesTest()
{
// First try removals with no impact
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault0_6());
IdentityPath path;
SrmDocument docFasta = document.ImportFasta(new StringReader(string.Format(TEXT_FASTA_YEAST_FRAGMENT, 1)),
false, IdentityPath.ROOT, out path);
AssertEx.IsDocumentState(docFasta, 1, 1, 11, 36);
var refinementSettings = new RefinementSettings {
RemoveDuplicatePeptides = true
};
SrmDocument docFasta2 = refinementSettings.Refine(docFasta);
Assert.AreSame(docFasta, docFasta2);
docFasta2 = docFasta.ImportFasta(new StringReader(string.Format(TEXT_FASTA_YEAST_FRAGMENT, 2)),
false, IdentityPath.ROOT, out path);
// Adding same sequence twice, even with different custom names is ignored
Assert.AreSame(docFasta, docFasta2);
// Try a successful removal of duplicates that leaves no peptides
SrmDocument docPeptides = document.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES1),
true, IdentityPath.ROOT, out path);
SrmDocument docPeptides2 = docPeptides.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES1),
true, IdentityPath.ROOT, out path);
AssertEx.IsDocumentState(docPeptides2, 2, 2, 26, 82);
SrmDocument docPeptides3 = refinementSettings.Refine(docPeptides2);
Assert.AreNotSame(docPeptides2, docPeptides3);
AssertEx.IsDocumentState(docPeptides3, 3, 2, 0, 0);
// Try again leaving a single peptide
docPeptides2 = docPeptides.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES1 + "\n" + TEXT_BOVINE_SINGLE_PEPTIDE),
true, IdentityPath.ROOT, out path);
docPeptides3 = refinementSettings.Refine(docPeptides2);
Assert.AreNotSame(docPeptides2, docPeptides3);
AssertEx.IsDocumentState(docPeptides3, 3, 2, 1, 3);
}
public void RefineResultsTest()
{
Settings.Default.RTCalculatorName = Settings.Default.RTScoreCalculatorList.GetDefaults().First().Name;
var document = InitRefineDocument(RefinementSettings.ConvertToSmallMoleculesMode.none);
// First check a few refinements which should not change the document
var refineSettings = new RefinementSettings {
RTRegressionThreshold = 0.3
};
Assert.AreSame(document, refineSettings.Refine(document));
refineSettings.RTRegressionThreshold = null;
refineSettings.DotProductThreshold = Statistics.AngleToNormalizedContrastAngle(0.1); // Convert form original cos(angle) dot-product
Assert.AreSame(document, refineSettings.Refine(document));
refineSettings.DotProductThreshold = null;
refineSettings.MinPeakFoundRatio = 0;
refineSettings.MaxPeakFoundRatio = 1.0;
Assert.AreSame(document, refineSettings.Refine(document));
refineSettings.MinPeakFoundRatio = refineSettings.MaxPeakFoundRatio = null;
// refineSettings.MaxPeakRank = 15; This will remove unmeasured transitions
Assert.AreSame(document, refineSettings.Refine(document));
// Remove nodes without results
refineSettings.MinPeptidesPerProtein = 1;
refineSettings.RemoveMissingResults = true;
var docRefined = refineSettings.Refine(document);
Assert.AreEqual(document.PeptideGroupCount, docRefined.PeptideGroupCount);
// First three children should be unchanged
for (int i = 0; i < 3; i++)
{
Assert.AreSame(document.Children[i], docRefined.Children[i]);
}
var nodePepGroupRefined = (PeptideGroupDocNode)docRefined.Children[3];
Assert.AreEqual(1, nodePepGroupRefined.MoleculeCount);
Assert.AreEqual(1, nodePepGroupRefined.TransitionGroupCount);
Assert.AreEqual(5, nodePepGroupRefined.TransitionCount);
// Filter for dot product, ignoring nodes without results
refineSettings.RemoveMissingResults = false;
double dotProductThreshold = Statistics.AngleToNormalizedContrastAngle(0.9); // Convert form original cos(angle) dot-product
refineSettings.DotProductThreshold = dotProductThreshold;
docRefined = refineSettings.Refine(document);
int missingResults = 0;
foreach (var nodeGroup in docRefined.PeptideTransitionGroups)
{
if (!nodeGroup.HasResults || nodeGroup.Results[0].IsEmpty)
{
missingResults++;
}
else
{
Assert.IsTrue(nodeGroup.Results[0][0].LibraryDotProduct >= dotProductThreshold);
}
}
Assert.AreNotEqual(0, missingResults);
Assert.IsTrue(missingResults < docRefined.PeptideTransitionGroupCount);
// Further refine with retention time refinement
refineSettings.RTRegressionThreshold = 0.95;
refineSettings.RTRegressionPrecision = 2; // Backward compatibility
var docRefinedRT = refineSettings.Refine(document);
Assert.AreNotEqual(docRefined.PeptideCount, docRefinedRT.PeptideCount);
// And peak count ratio
refineSettings.MinPeakFoundRatio = 1.0;
var docRefinedRatio = refineSettings.Refine(document);
Assert.AreNotEqual(docRefinedRT.PeptideCount, docRefinedRatio.PeptideCount);
Assert.IsTrue(ArrayUtil.EqualsDeep(docRefinedRatio.Children,
refineSettings.Refine(docRefinedRT).Children));
foreach (var nodeGroup in docRefinedRatio.PeptideTransitionGroups)
{
Assert.IsTrue(nodeGroup.HasResults);
Assert.IsTrue(nodeGroup.HasLibInfo);
Assert.AreEqual(1.0, nodeGroup.Results[0][0].PeakCountRatio);
}
Assert.AreEqual(2, docRefinedRatio.PeptideGroupCount);
Assert.AreEqual(7, docRefinedRatio.PeptideTransitionGroupCount);
// Pick only most intense transtions
refineSettings.MaxPeakRank = 4;
var docRefineMaxPeaks = refineSettings.Refine(document);
Assert.AreEqual(28, docRefineMaxPeaks.PeptideTransitionCount);
// Make sure the remaining peaks really started as the right rank,
// and did not change.
var dictIdTran = new Dictionary <int, TransitionDocNode>();
foreach (var nodeTran in document.PeptideTransitions)
{
dictIdTran.Add(nodeTran.Id.GlobalIndex, nodeTran);
}
foreach (var nodeGroup in docRefineMaxPeaks.PeptideTransitionGroups)
{
Assert.AreEqual(refineSettings.MaxPeakRank, nodeGroup.TransitionCount);
foreach (TransitionDocNode nodeTran in nodeGroup.Children)
{
int rank = nodeTran.Results[0][0].Rank;
Assert.IsTrue(rank <= refineSettings.MaxPeakRank);
var nodeTranOld = dictIdTran[nodeTran.Id.GlobalIndex];
Assert.AreEqual(nodeTranOld.Results[0][0].Rank, nodeTran.Results[0][0].Rank);
}
}
// Pick only most intenst peptides
refineSettings = new RefinementSettings {
MaxPepPeakRank = 5
};
var docRefinePepMaxPeaks = refineSettings.Refine(document);
// 4 groups, one unmeasured and one with only 3 peptides
Assert.AreEqual(13, docRefinePepMaxPeaks.PeptideCount);
Assert.AreEqual(docRefinePepMaxPeaks.PeptideCount, docRefinePepMaxPeaks.PeptideTransitionGroupCount);
// Add heavy labeled precursors for everything
var settingsNew = docRefineMaxPeaks.Settings.ChangeTransitionFilter(f => f.ChangeAutoSelect(false));
settingsNew = settingsNew.ChangePeptideModifications(m => m.ChangeModifications(IsotopeLabelType.heavy, new[]
{
new StaticMod("13C K", "K", ModTerminus.C, null, LabelAtoms.C13, null, null),
new StaticMod("13C R", "R", ModTerminus.C, null, LabelAtoms.C13, null, null),
}));
var docPrepareAdd = docRefineMaxPeaks.ChangeSettings(settingsNew);
refineSettings = new RefinementSettings {
RefineLabelType = IsotopeLabelType.heavy, AddLabelType = true
};
var docHeavy = refineSettings.Refine(docPrepareAdd);
Assert.AreEqual(docRefineMaxPeaks.PeptideTransitionCount * 2, docHeavy.PeptideTransitionCount);
// Verify that the precursors were added with the right transitions
foreach (var nodePep in docHeavy.Peptides)
{
Assert.AreEqual(2, nodePep.Children.Count);
var lightGroup = (TransitionGroupDocNode)nodePep.Children[0];
Assert.AreEqual(IsotopeLabelType.light, lightGroup.TransitionGroup.LabelType);
var heavyGroup = (TransitionGroupDocNode)nodePep.Children[1];
Assert.AreEqual(IsotopeLabelType.heavy, heavyGroup.TransitionGroup.LabelType);
Assert.AreEqual(lightGroup.TransitionGroup.PrecursorAdduct,
heavyGroup.TransitionGroup.PrecursorAdduct);
Assert.AreEqual(lightGroup.Children.Count, heavyGroup.Children.Count);
for (int i = 0; i < lightGroup.Children.Count; i++)
{
var lightTran = (TransitionDocNode)lightGroup.Children[i];
var heavyTran = (TransitionDocNode)heavyGroup.Children[i];
Assert.AreEqual(lightTran.Transition.FragmentIonName, heavyTran.Transition.FragmentIonName);
}
}
}
public void RunTestFindNode(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules)
{
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none)
{
TestDirectoryName = asSmallMolecules.ToString();
}
SrmDocument doc = CreateStudy7Doc();
doc = new RefinementSettings().ConvertToSmallMolecules(doc, TestDirectoryName, asSmallMolecules);
var displaySettings = new DisplaySettings(null, false, 0, 0); //, ProteinDisplayMode.ByName);
// Find every other transition, searching down.
List <TransitionDocNode> listTransitions = doc.MoleculeTransitions.ToList();
var pathFound = doc.GetPathTo(0, 0);
int i;
for (i = 0; i < doc.MoleculeTransitionCount; i += 2)
{
pathFound = doc.SearchDocumentForString(pathFound, String.Format("{0:F04}", listTransitions[i].Mz), displaySettings, false, false);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.Transitions, i), pathFound);
}
// Test wrapping in search down.
pathFound = doc.SearchDocumentForString(pathFound, String.Format("{0:F04}", listTransitions[0].Mz), displaySettings, false, false);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.Transitions, 0), pathFound);
// Find every other peptide searching up while for each finding one of its children searching down.
pathFound = doc.LastNodePath;
List <PeptideDocNode> listPeptides = new List <PeptideDocNode>();
listPeptides.AddRange(doc.Molecules);
List <TransitionGroupDocNode> listTransitionGroups = new List <TransitionGroupDocNode>();
listTransitionGroups.AddRange(doc.MoleculeTransitionGroups);
for (int x = doc.MoleculeCount; x > 0; x -= 2)
{
// Test case insensitivity.
pathFound = doc.SearchDocumentForString(pathFound, listPeptides[x - 1].ToString().ToLower(), displaySettings, true, false);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.Molecules, x - 1), pathFound);
// Test parents can find children.
pathFound = doc.SearchDocumentForString(pathFound, String.Format("{0:F04}", listTransitionGroups[x * 2 - 1].PrecursorMz.Value), displaySettings,
false, true);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.TransitionGroups, x * 2 - 1), pathFound);
// Test Children can find parents.
pathFound = doc.SearchDocumentForString(pathFound, listPeptides[x - 1].ToString().ToLower(), displaySettings, true, false);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.Molecules, x - 1), pathFound);
}
// Test wrapping in search up.
pathFound = doc.SearchDocumentForString(pathFound, String.Format("{0:F04}", listTransitionGroups[listTransitionGroups.Count - 1].PrecursorMz.Value),
displaySettings, false, true);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.TransitionGroups, listTransitionGroups.Count - 1), pathFound);
// Test children can find other parents.
pathFound = doc.SearchDocumentForString(pathFound, listPeptides[0].ToString().ToLowerInvariant(), displaySettings, true, false);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.Molecules, 0), pathFound);
// Test forward and backward searching in succession
const string heavyText = "heavy";
int countHeavyForward = CountOccurrances(doc, heavyText, displaySettings, false, true);
Assert.IsTrue(countHeavyForward > 0);
Assert.AreEqual(countHeavyForward, CountOccurrances(doc, heavyText, displaySettings, true, true));
// More tests of case insensitive searching
Assert.AreEqual(0, CountOccurrances(doc, heavyText.ToUpperInvariant(), displaySettings, false, true));
Assert.AreEqual(countHeavyForward, CountOccurrances(doc, heavyText.ToUpperInvariant(), displaySettings, false, false));
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
Assert.AreEqual(1, CountOccurrances(doc, "hgflpr", displaySettings, true, false));
}
// Test mismatched transitions finder
var missmatchFinder = new FindOptions().ChangeCustomFinders(new[] { new MismatchedIsotopeTransitionsFinder() });
Assert.AreEqual(4, CountOccurrances(doc, missmatchFinder, displaySettings));
var docRemoved = (SrmDocument)doc.RemoveChild(doc.Children[1]).RemoveChild(doc.Children[2]);
Assert.AreEqual(0, CountOccurrances(docRemoved, missmatchFinder, displaySettings));
var refineRemoveHeavy = new RefinementSettings {
RefineLabelType = IsotopeLabelType.heavy
};
var docLight = refineRemoveHeavy.Refine(doc);
Assert.AreEqual(0, CountOccurrances(docLight, missmatchFinder, displaySettings));
var refineRemoveLight = new RefinementSettings {
RefineLabelType = IsotopeLabelType.light
};
var docHeavy = refineRemoveLight.Refine(doc);
Assert.AreEqual(0, CountOccurrances(docHeavy, missmatchFinder, displaySettings));
var docMulti = ResultsUtil.DeserializeDocument("MultiLabel.sky", GetType());
docMulti = (new RefinementSettings()).ConvertToSmallMolecules(docMulti, TestContext.TestDir, asSmallMolecules);
Assert.AreEqual(0, CountOccurrances(docMulti, missmatchFinder, displaySettings));
var pathTranMultiRemove = docMulti.GetPathTo((int)SrmDocument.Level.Transitions, 7);
var tranMultiRemove = docMulti.FindNode(pathTranMultiRemove);
var docMultiRemoved = (SrmDocument)docMulti.RemoveChild(pathTranMultiRemove.Parent, tranMultiRemove);
Assert.AreEqual(2, CountOccurrances(docMultiRemoved, missmatchFinder, displaySettings));
var tranGroupMultiRemove = docMulti.FindNode(pathTranMultiRemove.Parent);
var docMultiGroupRemoved = (SrmDocument)
docMulti.RemoveChild(pathTranMultiRemove.Parent.Parent, tranGroupMultiRemove);
Assert.AreEqual(0, CountOccurrances(docMultiGroupRemoved, missmatchFinder, displaySettings));
}
private void DoFullScanFilterTest(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules,
out List <SrmDocument> docCheckpoints, bool centroided = false)
{
docCheckpoints = new List <SrmDocument>();
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath = testFilesDir.GetTestPath("BSA_Protea_label_free_20100323_meth3_multi.sky");
var expectedPepCount = 7;
var expectedTransGroupCount = 7;
var expectedTransCount = 49;
var doc = InitFullScanDocument(ref docPath, 2, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules);
if (centroided && ExtensionTestContext.CanImportThermoRaw)
{
const double ppm20 = 20.0;
doc = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorResolution(FullScanMassAnalyzerType.centroided, ppm20, 0)));
}
using (var docContainer = new ResultsTestDocumentContainer(doc, docPath))
{
// Import the first RAW file (or mzML for international)
string rawPath = testFilesDir.GetTestPath("ah_20101011y_BSA_MS-MS_only_5-2" +
ExtensionTestContext.ExtThermoRaw);
var measuredResults = new MeasuredResults(new[] { new ChromatogramSet("Single", new[] { new MsDataFilePath(rawPath) }) });
SrmDocument docResults = docContainer.ChangeMeasuredResults(measuredResults, 3, 3, 21);
docCheckpoints.Add(docResults);
// Refilter allowing multiple precursors per spectrum
SrmDocument docMulti = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(
fs => fs.ChangeAcquisitionMethod(FullScanAcquisitionMethod.DIA, new IsolationScheme("Test", 2))));
AssertEx.Serializable(docMulti, AssertEx.DocumentCloned);
// Release data cache file
Assume.IsTrue(docContainer.SetDocument(docMulti, docResults));
// And remove it
FileEx.SafeDelete(Path.ChangeExtension(docPath, ChromatogramCache.EXT));
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, 6, 6, 38));
// Import full scan Orbi-Velos data
docPath = testFilesDir.GetTestPath("BSA_Protea_label_free_20100323_meth3_long_acc_template.sky");
expectedPepCount = 3;
expectedTransGroupCount = 3;
expectedTransCount = 21;
doc = InitFullScanDocument(ref docPath, 1, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules);
docCheckpoints.Add(doc);
Assume.AreEqual(FullScanMassAnalyzerType.orbitrap, doc.Settings.TransitionSettings.FullScan.ProductMassAnalyzer);
// Make sure saving this type of document works
AssertEx.Serializable(doc, AssertEx.DocumentCloned);
Assume.IsTrue(docContainer.SetDocument(doc, docContainer.Document));
rawPath = testFilesDir.GetTestPath("ah_20101029r_BSA_CID_FT_centroid_3uscan_3" +
ExtensionTestContext.ExtThermoRaw);
measuredResults = new MeasuredResults(new[] { new ChromatogramSet("Accurate", new[] { rawPath }) });
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, 3, 3, 21));
// Import LTQ data with MS1 and MS/MS
docPath = testFilesDir.GetTestPath("BSA_Protea_label_free_20100323_meth3_test4.sky");
expectedPepCount = 3;
expectedTransGroupCount = 4;
expectedTransCount = 32;
doc = InitFullScanDocument(ref docPath, 3, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules);
Assume.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.ProductMassAnalyzer);
Assume.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.PrecursorMassAnalyzer);
docCheckpoints.Add(doc);
var docBoth = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangeAcquisitionMethod(FullScanAcquisitionMethod.Targeted, null)
.ChangePrecursorResolution(FullScanMassAnalyzerType.qit, TransitionFullScan.DEFAULT_RES_QIT, null)));
docCheckpoints.Add(docBoth);
AssertEx.Serializable(docBoth, AssertEx.DocumentCloned);
Assume.IsTrue(docContainer.SetDocument(docBoth, docContainer.Document));
string dataPath = testFilesDir.GetTestPath("klc_20100329v_Protea_Peptide_Curve_200fmol_uL_tech1.mzML");
var listResults = new List <ChromatogramSet>
{
new ChromatogramSet("MS1 and MS/MS", new[] { dataPath }),
};
measuredResults = new MeasuredResults(listResults.ToArray());
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, expectedPepCount, expectedTransGroupCount, expectedTransCount - 6));
// The mzML was filtered for the m/z range 410 to 910.
foreach (var nodeTran in docContainer.Document.MoleculeTransitions)
{
Assume.IsTrue(nodeTran.HasResults);
Assume.IsNotNull(nodeTran.Results[0]);
if (410 > nodeTran.Mz || nodeTran.Mz > 910)
{
Assume.IsTrue(nodeTran.Results[0][0].IsForcedIntegration);
}
else
{
Assume.IsFalse(nodeTran.Results[0][0].IsForcedIntegration);
}
}
// Import LTQ data with MS1 and MS/MS using multiple files for a single replicate
listResults.Add(new ChromatogramSet("Multi-file", new[]
{
testFilesDir.GetTestPath("both_DRV.mzML"),
testFilesDir.GetTestPath("both_KVP.mzML"),
}));
measuredResults = new MeasuredResults(listResults.ToArray());
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, expectedPepCount - 1, expectedTransGroupCount - 1, expectedTransCount - 6));
if (asSmallMolecules == RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
return; // Can't work with isotope distributions when we don't have ion formulas
}
int indexResults = listResults.Count - 1;
var matchIdentifierDRV = "DRV";
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none)
{
matchIdentifierDRV = RefinementSettings.TestingConvertedFromProteomicPeptideNameDecorator + matchIdentifierDRV;
}
int index = 0;
foreach (var nodeTran in docContainer.Document.MoleculeTransitions)
{
Assume.IsTrue(nodeTran.HasResults);
Assume.AreEqual(listResults.Count, nodeTran.Results.Count);
var peptide = nodeTran.Transition.Group.Peptide;
if (peptide.IsCustomMolecule && index == 24)
{
// Conversion to small molecule loses some of the nuance of "Sequence" vs "FastaSequence", comparisons are inexact
Assume.AreEqual("pep_DRVY[+80.0]IHPF", nodeTran.PrimaryCustomIonEquivalenceKey);
break;
}
// DRV without FASTA sequence should not have data for non-precursor transitions
if (!peptide.TextId.StartsWith(matchIdentifierDRV) ||
(!peptide.IsCustomMolecule && !peptide.Begin.HasValue))
{
Assume.IsNotNull(nodeTran.Results[indexResults]);
Assume.IsFalse(nodeTran.Results[indexResults][0].IsEmpty);
}
else if (nodeTran.Transition.IonType != IonType.precursor)
{
Assert.IsTrue(nodeTran.Results[indexResults].IsEmpty);
}
else
{
// Random, bogus peaks chosen in both files
Assume.IsNotNull(nodeTran.Results[indexResults]);
Assume.AreEqual(2, nodeTran.Results[indexResults].Count);
Assume.IsFalse(nodeTran.Results[indexResults][0].IsEmpty);
Assume.IsFalse(nodeTran.Results[indexResults][1].IsEmpty);
}
index++;
}
// Verify handling of bad request for vendor centroided data - out-of-range PPM
docPath = testFilesDir.GetTestPath("Yeast_HI3 Peptides_test.sky");
expectedPepCount = 2;
expectedTransGroupCount = 2;
expectedTransCount = 2;
doc = InitFullScanDocument(ref docPath, 2, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules);
Assume.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.ProductMassAnalyzer);
Assume.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.PrecursorMassAnalyzer);
var docBad = doc;
AssertEx.ThrowsException <InvalidDataException>(() =>
docBad.ChangeSettings(docBad.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 1, IsotopeEnrichmentsList.DEFAULT)
.ChangePrecursorResolution(FullScanMassAnalyzerType.centroided, 50 * 1000, 400))),
string.Format(Resources.TransitionFullScan_ValidateRes_Mass_accuracy_must_be_between__0__and__1__for_centroided_data_,
TransitionFullScan.MIN_CENTROID_PPM, TransitionFullScan.MAX_CENTROID_PPM));
// Verify relationship between PPM and resolving power
const double ppm = 20.0; // Should yield same filter width as resolving power 50,000 in TOF
var docNoCentroid = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 1, IsotopeEnrichmentsList.DEFAULT)
.ChangePrecursorResolution(FullScanMassAnalyzerType.centroided, ppm, 0)));
AssertEx.Serializable(docNoCentroid, AssertEx.DocumentCloned);
Assume.IsTrue(docContainer.SetDocument(docNoCentroid, docContainer.Document));
const double mzTest = 400.0;
var filterWidth = docNoCentroid.Settings.TransitionSettings.FullScan.GetPrecursorFilterWindow(mzTest);
Assume.AreEqual(mzTest * 2.0 * ppm * 1E-6, filterWidth);
// Verify relationship between normal and high-selectivity extraction
var docTofNormal = docNoCentroid.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorResolution(FullScanMassAnalyzerType.tof, 50 * 1000, null)));
AssertEx.Serializable(docTofNormal, AssertEx.DocumentCloned);
var docTofSelective = docTofNormal.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorResolution(FullScanMassAnalyzerType.tof, 25 * 1000, null)
.ChangeUseSelectiveExtraction(true)));
AssertEx.Serializable(docTofSelective, AssertEx.DocumentCloned);
var filterWidthTof = docTofNormal.Settings.TransitionSettings.FullScan.GetPrecursorFilterWindow(mzTest);
var filterWidthSelective = docTofSelective.Settings.TransitionSettings.FullScan.GetPrecursorFilterWindow(mzTest);
Assume.AreEqual(filterWidth, filterWidthTof);
Assume.AreEqual(filterWidth, filterWidthSelective);
// Verify handling of bad request for vendor centroided data - ask for centroiding in mzML
const string fileName = "S_2_LVN.mzML";
var filePath = testFilesDir.GetTestPath(fileName);
AssertEx.ThrowsException <AssertFailedException>(() =>
{
listResults = new List <ChromatogramSet> {
new ChromatogramSet("rep1", new[] { new MsDataFilePath(filePath) }),
};
docContainer.ChangeMeasuredResults(new MeasuredResults(listResults.ToArray()), 1, 1, 1);
},
string.Format(Resources.NoCentroidedDataException_NoCentroidedDataException_No_centroided_data_available_for_file___0_____Adjust_your_Full_Scan_settings_, filePath));
// Import FT data with only MS1
docPath = testFilesDir.GetTestPath("Yeast_HI3 Peptides_test.sky");
expectedPepCount = 2;
expectedTransGroupCount = 2;
expectedTransCount = 2;
doc = InitFullScanDocument(ref docPath, 2, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules);
Assume.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.ProductMassAnalyzer);
Assume.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.PrecursorMassAnalyzer);
var docMs1 = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 1, IsotopeEnrichmentsList.DEFAULT)
.ChangePrecursorResolution(FullScanMassAnalyzerType.tof, 50 * 1000, null)));
Assume.AreEqual(filterWidth, docMs1.Settings.TransitionSettings.FullScan.GetPrecursorFilterWindow(mzTest));
docMs1 = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 1, IsotopeEnrichmentsList.DEFAULT)
.ChangePrecursorResolution(FullScanMassAnalyzerType.ft_icr, 50 * 1000, mzTest)));
AssertEx.Serializable(docMs1, AssertEx.DocumentCloned);
Assume.IsTrue(docContainer.SetDocument(docMs1, docContainer.Document));
const string rep1 = "rep1";
listResults = new List <ChromatogramSet>
{
new ChromatogramSet(rep1, new[] { filePath }),
};
measuredResults = new MeasuredResults(listResults.ToArray());
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, 1, 1, 1));
// Because of the way the mzML files were filtered, all of the LVN peaks should be present
// in the first replicate, and all of the NVN peaks should be present in the other.
var matchIdentifierLVN = "LVN";
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none)
{
matchIdentifierLVN = RefinementSettings.TestingConvertedFromProteomicPeptideNameDecorator + matchIdentifierLVN;
}
foreach (var nodeTranGroup in docContainer.Document.MoleculeTransitionGroups)
{
foreach (var docNode in nodeTranGroup.Children)
{
var nodeTran = (TransitionDocNode)docNode;
Assume.IsTrue(nodeTran.HasResults);
Assume.AreEqual(1, nodeTran.Results.Count);
if (nodeTran.Transition.Group.Peptide.Target.ToString().StartsWith(matchIdentifierLVN))
{
Assume.IsFalse(nodeTran.Results[0][0].IsEmpty);
}
else
{
Assume.IsTrue(nodeTran.Results[0][0].IsEmpty);
}
}
}
const string rep2 = "rep2";
listResults.Add(new ChromatogramSet(rep2, new[] { testFilesDir.GetTestPath("S_2_NVN.mzML") }));
measuredResults = new MeasuredResults(listResults.ToArray());
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, 1, 1, 1));
// Because of the way the mzML files were filtered, all of the LVN peaks should be present
// in the first replicate, and all of the NVN peaks should be present in the other.
foreach (var nodeTranGroup in docContainer.Document.MoleculeTransitionGroups)
{
foreach (var docNode in nodeTranGroup.Children)
{
var nodeTran = (TransitionDocNode)docNode;
Assume.IsTrue(nodeTran.HasResults);
Assume.AreEqual(2, nodeTran.Results.Count);
if (nodeTran.Transition.Group.Peptide.Target.ToString().StartsWith(matchIdentifierLVN))
{
Assume.IsTrue(nodeTran.Results[1][0].IsEmpty);
}
else
{
Assume.IsFalse(nodeTran.Results[1][0].IsEmpty);
}
}
}
// Chromatograms should be present in the cache for a number of isotopes.
var docMs1Isotopes = docContainer.Document.ChangeSettings(doc.Settings
.ChangeTransitionFullScan(fs => fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count,
3, IsotopeEnrichmentsList.DEFAULT))
.ChangeTransitionFilter(filter => filter.ChangePeptideIonTypes(new[] { IonType.precursor })
.ChangeSmallMoleculeIonTypes(new[] { IonType.precursor })));
docCheckpoints.Add(docMs1Isotopes);
AssertEx.IsDocumentState(docMs1Isotopes, null, 2, 2, 2); // Need to reset auto-manage for transitions
var refineAutoSelect = new RefinementSettings {
AutoPickChildrenAll = PickLevel.transitions
};
docMs1Isotopes = refineAutoSelect.Refine(docMs1Isotopes);
AssertEx.IsDocumentState(docMs1Isotopes, null, 2, 2, 6);
AssertResult.IsDocumentResultsState(docMs1Isotopes, rep1, 1, 1, 0, 3, 0);
AssertResult.IsDocumentResultsState(docMs1Isotopes, rep2, 1, 1, 0, 3, 0);
docCheckpoints.Add(docMs1Isotopes);
// Add M-1 transitions, and verify that they have chromatogram data also, but
// empty peaks in all cases
var docMs1All = docMs1Isotopes.ChangeSettings(docMs1Isotopes.Settings
.ChangeTransitionFullScan(fs => fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Percent,
0, IsotopeEnrichmentsList.DEFAULT))
.ChangeTransitionIntegration(i => i.ChangeIntegrateAll(false))); // For compatibility with v2.5 and earlier
docCheckpoints.Add(docMs1All);
AssertEx.IsDocumentState(docMs1All, null, 2, 2, 10);
AssertResult.IsDocumentResultsState(docMs1All, rep1, 1, 1, 0, 4, 0);
AssertResult.IsDocumentResultsState(docMs1All, rep2, 1, 1, 0, 4, 0);
var ms1AllTranstions = docMs1All.MoleculeTransitions.ToArray();
var tranM1 = ms1AllTranstions[0];
Assert.AreEqual(-1, tranM1.Transition.MassIndex);
Assert.IsTrue(!tranM1.Results[0].IsEmpty && !tranM1.Results[1].IsEmpty);
Assert.IsTrue(tranM1.Results[0][0].IsEmpty && tranM1.Results[1][0].IsForcedIntegration);
tranM1 = ms1AllTranstions[5];
Assert.AreEqual(-1, tranM1.Transition.MassIndex);
Assert.IsTrue(!tranM1.Results[0].IsEmpty && !tranM1.Results[1].IsEmpty);
Assert.IsTrue(tranM1.Results[0][0].IsForcedIntegration && tranM1.Results[1][0].IsEmpty);
}
}