private void Import(ResultsTestDocumentContainer docContainer, string resultsPath, double minMz, double maxMz)
{
var measuredResults = new MeasuredResults(new[] { new ChromatogramSet("Single", new[] { resultsPath }) });
docContainer.ChangeMeasuredResults(measuredResults, 1, 1, 3);
// Check expected Mz range.
foreach (var nodeTran in docContainer.Document.MoleculeTransitions)
{
Assert.IsTrue(nodeTran.HasResults, "No results for transition Mz: {0}", nodeTran.Mz);
if (nodeTran.Results[0].IsEmpty)
{
continue;
}
//Assert.IsNotNull(nodeTran.Results[0], "Null results for transition Mz: {0}", nodeTran.Mz);
if (minMz > nodeTran.Mz || nodeTran.Mz > maxMz)
{
Assert.IsTrue(nodeTran.Results[0][0].IsEmpty, "Non-empty transition Mz: {0}", nodeTran.Mz);
}
else
{
Assert.IsFalse(nodeTran.Results[0][0].IsEmpty, "Empty transition Mz: {0}", nodeTran.Mz);
}
}
}
public void TestCollectStatistics()
{
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath = testFilesDir.GetTestPath("BSA_Protea_label_free_20100323_meth3_multi.sky");
SrmDocument doc = ResultsUtil.DeserializeDocument(docPath);
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[] { MsDataFileUri.Parse(rawPath) }) });
SrmDocument docResults = docContainer.ChangeMeasuredResults(measuredResults, 3, 3, 21);
ChromCacheMinimizer chromCacheMinimizer =
docResults.Settings.MeasuredResults.GetChromCacheMinimizer(docResults);
ChromCacheMinimizer.Settings settings =
new ChromCacheMinimizer.Settings().SetDiscardUnmatchedChromatograms(true);
ChromCacheMinimizer.MinStatistics minStatistics = null;
chromCacheMinimizer.Minimize(settings, s => minStatistics = s, null);
Assert.AreEqual(100, minStatistics.PercentComplete);
Assert.AreEqual(1.0, minStatistics.MinimizedRatio);
var docMissingFirstPeptide =
(SrmDocument)
docResults.ReplaceChild(
docResults.PeptideGroups.First().RemoveChild(docResults.PeptideGroups.First().Children[0]));
var docWithOnlyFirstPeptide =
(SrmDocument)
docResults.ReplaceChild(
docResults.PeptideGroups.First().ChangeChildren(new[] { docResults.PeptideGroups.First().Children[0] }));
ChromCacheMinimizer.MinStatistics statsMissingFirstProtein = null;
ChromCacheMinimizer.MinStatistics statsWithOnlyFirstProtein = null;
settings = settings.SetDiscardUnmatchedChromatograms(true);
ChromCacheMinimizer minimizerMissingFirstProtein =
docMissingFirstPeptide.Settings.MeasuredResults.GetChromCacheMinimizer(docMissingFirstPeptide);
ChromCacheMinimizer minimizerWithOnlyFirstProtein =
docWithOnlyFirstPeptide.Settings.MeasuredResults.GetChromCacheMinimizer(docWithOnlyFirstPeptide);
minimizerMissingFirstProtein.Minimize(settings, s => statsMissingFirstProtein = s, null);
minimizerWithOnlyFirstProtein.Minimize(settings, s => statsWithOnlyFirstProtein = s, null);
Assert.AreEqual(100, statsMissingFirstProtein.PercentComplete);
Assert.AreEqual(100, statsWithOnlyFirstProtein.PercentComplete);
Assert.AreEqual(1.0, statsMissingFirstProtein.MinimizedRatio + statsWithOnlyFirstProtein.MinimizedRatio,
.00001);
settings = settings.SetDiscardUnmatchedChromatograms(false);
ChromCacheMinimizer.MinStatistics statsMissingFirstProteinKeepAll = null;
ChromCacheMinimizer.MinStatistics statsWithOnlyFirstProteinKeepAll = null;
minimizerMissingFirstProtein.Minimize(settings, s => statsMissingFirstProteinKeepAll = s, null);
minimizerWithOnlyFirstProtein.Minimize(settings, s => statsWithOnlyFirstProteinKeepAll = s, null);
Assert.AreEqual(100, statsMissingFirstProteinKeepAll.PercentComplete);
Assert.AreEqual(1.0, statsMissingFirstProteinKeepAll.MinimizedRatio);
Assert.AreEqual(100, statsWithOnlyFirstProteinKeepAll.PercentComplete);
Assert.AreEqual(1.0, statsWithOnlyFirstProteinKeepAll.MinimizedRatio);
docContainer.Release();
}
private void ExportImport(ResultsTestDocumentContainer docContainer, string resultsPath)
{
var optRegression = docContainer.Document.Settings.TransitionSettings.Prediction.CollisionEnergy;
int optSteps = optRegression.StepCount * 2 + 1;
int optSteps1 = optSteps - 1; // First precursor is below 10 volts CE for 1 step
int optSteps2 = optSteps - 3; // Second precursor is below 10 volts CE for 3 steps
// First export
var exporter = new AbiMassListExporter(docContainer.Document)
{
OptimizeType = ExportOptimize.CE,
OptimizeStepCount = optRegression.StepCount,
OptimizeStepSize = optRegression.StepSize
};
string tranListPath = Path.ChangeExtension(docContainer.DocumentFilePath, TextUtil.EXT_CSV);
exporter.Export(tranListPath);
// Make sure line count matches expectations for steps below 10 volts CE
Assert.AreEqual(5 * optSteps1 + 5 * optSteps2, File.ReadAllLines(tranListPath).Length);
// Then import
var resultsUri = new MsDataFilePath(resultsPath);
var chromSet = new ChromatogramSet("Optimize", new[] { resultsUri }, Annotations.EMPTY, optRegression);
var measuredResults = new MeasuredResults(new[] { chromSet });
docContainer.ChangeMeasuredResults(measuredResults, 2, optSteps1 + optSteps2, 5 * optSteps1 + 5 * optSteps2);
// Check expected optimization data with missing values for steps below 10 volts CE
int expectedMissingSteps = optSteps - optSteps1;
foreach (var nodeGroup in docContainer.Document.MoleculeTransitionGroups)
{
foreach (var nodeTran in nodeGroup.Transitions)
{
Assert.IsTrue(nodeTran.HasResults, "No results for transition Mz: {0}", nodeTran.Mz);
Assert.IsNotNull(nodeTran.Results[0]);
Assert.AreEqual(optSteps, nodeTran.Results[0].Count);
for (int i = 0; i < optSteps; i++)
{
if (i < expectedMissingSteps)
{
Assert.IsTrue(nodeTran.Results[0][i].IsEmpty);
}
else
{
Assert.IsFalse(nodeTran.Results[0][i].IsEmpty);
}
}
}
expectedMissingSteps = optSteps - optSteps2;
}
}
public void DoAsymmetricIsolationTest(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules)
{
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none && !RunSmallMoleculeTestVersions)
{
Console.Write(MSG_SKIPPING_SMALLMOLECULE_TEST_VERSION);
return;
}
TestSmallMolecules = false; // We test small molecules explicitly in this test
LocalizationHelper.InitThread(); // TODO: All unit tests should be correctly initialized
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath = testFilesDir.GetTestPath("TROUBLED_File.sky");
string cachePath = ChromatogramCache.FinalPathForName(docPath, null);
FileEx.SafeDelete(cachePath);
SrmDocument doc = ResultsUtil.DeserializeDocument(docPath);
var refine = new RefinementSettings();
doc = refine.ConvertToSmallMolecules(doc, testFilesDir.FullPath, asSmallMolecules);
const int expectedMoleculeCount = 1; // At first small molecules did not support multiple label types
AssertEx.IsDocumentState(doc, null, 1, expectedMoleculeCount, 2, 6);
using (var docContainer = new ResultsTestDocumentContainer(doc, docPath))
{
// Import the first RAW file (or mzML for international)
string rawPath = testFilesDir.GetTestPath("Rush_p3_96_21May16_Smeagol.mzML");
var measuredResults = new MeasuredResults(new[] { new ChromatogramSet("Single", new[] { rawPath }) });
{
// Import with symmetric isolation window
var docResults =
docContainer.ChangeMeasuredResults(measuredResults, expectedMoleculeCount, 1, 1, 3, 3);
var nodeGroup = docResults.MoleculeTransitionGroups.First();
double ratio = nodeGroup.Results[0][0].Ratio ?? 0;
// The expected ratio is 1.0, but the symmetric isolation window should produce poor results
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.masses_only) // Can't use labels without a formula
{
Assert.AreEqual(0.008, ratio, 0.001);
}
}
}
testFilesDir.Dispose();
}
private void Import(ResultsTestDocumentContainer docContainer, string resultsPath, bool optFlag)
{
var optRegression = optFlag ? docContainer.Document.Settings.TransitionSettings.Prediction.CollisionEnergy : null;
int optSteps = optRegression != null ? optRegression.StepCount * 2 + 1 : 1;
var resultsUri = new MsDataFilePath(resultsPath);
var chromSet = new ChromatogramSet("Optimize", new[] { resultsUri }, Annotations.EMPTY, optRegression);
var measuredResults = new MeasuredResults(new[] { chromSet });
docContainer.ChangeMeasuredResults(measuredResults, 1, 1 * optSteps, 3 * optSteps);
// Check expected optimization data.
foreach (var nodeTran in docContainer.Document.MoleculeTransitions)
{
Assert.IsTrue(nodeTran.HasResults, "No results for transition Mz: {0}", nodeTran.Mz);
Assert.IsNotNull(nodeTran.Results[0]);
Assert.AreEqual(optSteps, nodeTran.Results[0].Count);
}
}
public void TestNoiseTimeLimit()
{
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath = testFilesDir.GetTestPath("BSA_Protea_label_free_20100323_meth3_multi.sky");
SrmDocument doc = ResultsUtil.DeserializeDocument(docPath);
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[] { rawPath }) });
SrmDocument docResults = docContainer.ChangeMeasuredResults(measuredResults, 3, 3, 21);
var tolerance = (float)docResults.Settings.TransitionSettings.Instrument.MzMatchTolerance;
ChromCacheMinimizer.Settings settings = new ChromCacheMinimizer.Settings()
.ChangeDiscardUnmatchedChromatograms(false)
.ChangeNoiseTimeRange(1.0);
string minimized1Path = testFilesDir.GetTestPath("NoiseTimeLimited1.sky");
string minimized2Path = testFilesDir.GetTestPath("NoiseTimeLimited2.sky");
using (var docContainerMinimized1Min = MinimizeCacheFile(docResults,
settings.ChangeNoiseTimeRange(1.0),
minimized1Path))
using (var docContainerMinimized2Min = MinimizeCacheFile(docResults,
settings.ChangeNoiseTimeRange(2.0),
minimized2Path))
{
SrmDocument docMinimized1Min = docContainerMinimized1Min.Document;
SrmDocument docMinimized2Min = docContainerMinimized2Min.Document;
ChromatogramSet chromSet1Min = docMinimized1Min.Settings.MeasuredResults.Chromatograms[0];
ChromatogramSet chromSet2Min = docMinimized2Min.Settings.MeasuredResults.Chromatograms[0];
ChromatogramSet chromSetOriginal = docResults.Settings.MeasuredResults.Chromatograms[0];
foreach (var pair in docResults.PeptidePrecursorPairs)
{
ChromatogramGroupInfo[] chromGroupsOriginal;
ChromatogramGroupInfo[] chromGroups1;
ChromatogramGroupInfo[] chromGroups2;
docMinimized1Min.Settings.MeasuredResults.TryLoadChromatogram(chromSet1Min,
pair.NodePep, pair.NodeGroup, tolerance, true, out chromGroups1);
docMinimized2Min.Settings.MeasuredResults.TryLoadChromatogram(chromSet2Min,
pair.NodePep, pair.NodeGroup, tolerance, true, out chromGroups2);
docResults.Settings.MeasuredResults.TryLoadChromatogram(chromSetOriginal,
pair.NodePep, pair.NodeGroup, tolerance, true, out chromGroupsOriginal);
Assert.AreEqual(chromGroups1.Length, chromGroups2.Length);
Assert.AreEqual(chromGroups1.Length, chromGroupsOriginal.Length);
for (int iChromGroup = 0; iChromGroup < chromGroups1.Length; iChromGroup++)
{
ChromatogramGroupInfo chromGroup1 = chromGroups1[iChromGroup];
ChromatogramGroupInfo chromGroup2 = chromGroups2[iChromGroup];
ChromatogramGroupInfo chromGroupOriginal = chromGroupsOriginal[iChromGroup];
var times = new[]
{
GetTimes(chromGroupOriginal)[0],
GetTimes(chromGroup2)[0],
GetTimes(chromGroup1)[0],
GetTimes(chromGroup1).Last(),
GetTimes(chromGroup2).Last(),
GetTimes(chromGroupOriginal).Last()
};
// The two minute window around the peak might overlap with either the start or end of the original chromatogram,
// but will never overlap with both.
Assert.IsTrue(GetTimes(chromGroup2)[0] > GetTimes(chromGroupOriginal)[0]
||
GetTimes(chromGroup2).Last() <
GetTimes(chromGroupOriginal).Last());
// If the two minute window does not overlap with the start/end of the original chromatogram, then the difference
// in time between the one minute window and the two minute window will be approximately 1 minute.
if (GetTimes(chromGroup2)[0] > GetTimes(chromGroupOriginal)[0])
{
Assert.AreEqual(GetTimes(chromGroup2)[0], GetTimes(chromGroup1)[0] - 1, .1);
}
if (GetTimes(chromGroup2).Last() <
GetTimes(chromGroupOriginal).Last())
{
Assert.AreEqual(GetTimes(chromGroup2).Last(),
GetTimes(chromGroup1).Last() + 1, .1);
}
float[] timesSorted = times.ToArray();
Array.Sort(timesSorted);
CollectionAssert.AreEqual(times, timesSorted);
}
}
}
}
}
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);
}
}
private static void TestInstrumentInfo(string resultsPath, string docCurrentPath)
{
var docCurrent = ResultsUtil.DeserializeDocument(docCurrentPath);
using (var docContainer = new ResultsTestDocumentContainer(docCurrent, docCurrentPath))
{
string replicateName = Path.GetFileNameWithoutExtension(resultsPath);
var lockMassParameters = new LockMassParameters(456.78, 567.89, 12.34);
var listChromatograms = new List <ChromatogramSet> {
new ChromatogramSet(replicateName, new[] { new MsDataFilePath(resultsPath, lockMassParameters) })
};
// Lockmass values are Waters only so don't expect them to be saved to the doc which has no Waters results
// So test the serialization here
var stringBuilder = new StringBuilder();
using (var xmlWriter = XmlWriter.Create(stringBuilder))
{
xmlWriter.WriteStartDocument();
xmlWriter.WriteStartElement("TestDocument");
xmlWriter.WriteElements(listChromatograms, new XmlElementHelper <ChromatogramSet>());
xmlWriter.WriteEndElement();
xmlWriter.WriteEndDocument();
}
var xmlReader = XmlReader.Create(new StringReader(stringBuilder.ToString()));
xmlReader.ReadStartElement();
var deserializedObjects = new List <ChromatogramSet>();
xmlReader.ReadElements(deserializedObjects);
Assert.AreEqual(1, deserializedObjects.Count);
var compare = deserializedObjects[0];
Assert.AreEqual(456.78, compare.MSDataFileInfos[0].FilePath.GetLockMassParameters().LockmassPositive.Value);
Assert.AreEqual(567.89, compare.MSDataFileInfos[0].FilePath.GetLockMassParameters().LockmassNegative.Value);
Assert.AreEqual(12.34, compare.MSDataFileInfos[0].FilePath.GetLockMassParameters().LockmassTolerance.Value);
Assert.AreEqual(listChromatograms[0], compare);
// We don't expect any new peptides/precursors/transitions added due to the imported results.
var docCurrentResults = docContainer.ChangeMeasuredResults(new MeasuredResults(listChromatograms), 0, 0, 0);
WriteDocument(docCurrentResults, docCurrentPath);
docCurrentResults = ResultsUtil.DeserializeDocument(docCurrentPath);
Assert.IsNotNull(docCurrentResults);
AssertEx.IsDocumentState(docCurrentResults, 0, 7, 11, 22, 66);
Assert.AreEqual(1, docCurrentResults.Settings.MeasuredResults.Chromatograms.Count);
XmlDocument xdoc = new XmlDocument();
xdoc.Load(docCurrentPath);
var replicateList = xdoc.SelectNodes("/srm_settings/settings_summary/measured_results/replicate");
Assert.IsNotNull(replicateList);
Assert.AreEqual(1, replicateList.Count);
var replicate = replicateList.Item(0);
Assert.IsNotNull(replicate);
var attribs = replicate.Attributes;
Assert.IsNotNull(attribs);
Assert.AreEqual(replicateName, attribs.GetNamedItem(DocumentSerializer.ATTR.name).Value);
var instrumentList = replicate.SelectNodes("sample_file/instrument_info_list/instrument_info");
Assert.IsNotNull(instrumentList);
Assert.AreEqual(1, instrumentList.Count);
var instrumentInfo = instrumentList.Item(0);
Assert.IsNotNull(instrumentInfo);
Assert.IsNotNull(instrumentInfo.Attributes);
// model
var model = instrumentInfo.SelectSingleNode(ChromatogramSet.EL.model.ToString());
Assert.IsNotNull(model);
Assert.IsNotNull(model.FirstChild);
Assert.IsTrue(model.FirstChild.NodeType == XmlNodeType.Text);
Assert.AreEqual("TSQ Vantage", model.FirstChild.Value);
// ion source
var ionsource = instrumentInfo.SelectSingleNode(ChromatogramSet.EL.ionsource.ToString());
Assert.IsNotNull(ionsource);
Assert.IsNotNull(ionsource.FirstChild);
Assert.AreEqual(ionsource.FirstChild.NodeType, XmlNodeType.Text);
Assert.AreEqual("nanoelectrospray", ionsource.FirstChild.Value);
// analyzer
var analyzer = instrumentInfo.SelectSingleNode(ChromatogramSet.EL.analyzer.ToString());
Assert.IsNotNull(analyzer);
Assert.IsNotNull(analyzer.FirstChild);
Assert.AreEqual(analyzer.FirstChild.NodeType, XmlNodeType.Text);
Assert.AreEqual("quadrupole/quadrupole/quadrupole", analyzer.FirstChild.Value);
// dectector
var detector = instrumentInfo.SelectSingleNode(ChromatogramSet.EL.detector.ToString());
Assert.IsNotNull(detector);
Assert.IsNotNull(detector.FirstChild);
Assert.AreEqual(detector.FirstChild.NodeType, XmlNodeType.Text);
Assert.AreEqual("electron multiplier", detector.FirstChild.Value);
}
}
public void DoAsymmetricIsolationTest(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules)
{
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none && !RunSmallMoleculeTestVersions)
{
Console.Write(MSG_SKIPPING_SMALLMOLECULE_TEST_VERSION);
return;
}
LocalizationHelper.InitThread(); // TODO: All unit tests should be correctly initialized
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath = testFilesDir.GetTestPath("Asym_DIA.sky");
string cachePath = ChromatogramCache.FinalPathForName(docPath, null);
FileEx.SafeDelete(cachePath);
SrmDocument doc = ResultsUtil.DeserializeDocument(docPath);
var refine = new RefinementSettings();
doc = refine.ConvertToSmallMolecules(doc, testFilesDir.FullPath, asSmallMolecules);
const int expectedMoleculeCount = 1; // At first small molecules did not support multiple charge states, and this was 2 for that test mode
AssertEx.IsDocumentState(doc, null, 1, expectedMoleculeCount, 2, 4);
var fullScanInitial = doc.Settings.TransitionSettings.FullScan;
Assert.IsTrue(fullScanInitial.IsEnabledMsMs);
Assert.AreEqual(FullScanAcquisitionMethod.DIA, fullScanInitial.AcquisitionMethod);
Assert.AreEqual(25, fullScanInitial.PrecursorFilter);
AssertEx.Serializable(doc);
using (var docContainer = new ResultsTestDocumentContainer(doc, docPath))
{
// Import the first RAW file (or mzML for international)
string rawPath = testFilesDir.GetTestPath("Asym_DIA_data.mzML");
var measuredResults = new MeasuredResults(new[] { new ChromatogramSet("Single", new[] { rawPath }) });
TransitionGroupDocNode nodeGroup;
double ratio;
const double poorRatio = 0.25;
const double fixedRatio = 1.05;
{
// Import with symmetric isolation window
SrmDocument docResults = docContainer.ChangeMeasuredResults(measuredResults, expectedMoleculeCount, 1, 1, 2, 2);
nodeGroup = docResults.MoleculeTransitionGroups.First();
ratio = nodeGroup.Results[0][0].Ratio ?? 0;
// The expected ratio is 1.0, but the symmetric isolation window should produce poor results
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.masses_only) // Can't use labels without a formula
{
Assert.AreEqual(poorRatio, ratio, 0.05);
}
// Revert to original document, and get rid of results cache
Assert.IsTrue(docContainer.SetDocument(doc, docResults, false));
FileEx.SafeDelete(testFilesDir.GetTestPath("Asym_DIA.skyd"));
}
{
// Import with asymmetric isolation window
SrmDocument docAsym = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fullScan =>
fullScan.ChangeAcquisitionMethod(fullScan.AcquisitionMethod, new IsolationScheme("Test asym", 5, 20))));
AssertEx.Serializable(docAsym);
Assert.IsTrue(docContainer.SetDocument(docAsym, doc, false));
SrmDocument docResults = docContainer.ChangeMeasuredResults(measuredResults, expectedMoleculeCount, 1, 1, 2, 2);
nodeGroup = docResults.MoleculeTransitionGroups.First();
ratio = nodeGroup.Results[0][0].Ratio ?? 0;
// Asymmetric should be a lot closer to 1.0
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.masses_only) // Can't use labels without a formula
{
Assert.AreEqual(fixedRatio, ratio, 0.05);
}
// Revert to original document, and get rid of results cache
Assert.IsTrue(docContainer.SetDocument(doc, docResults, false));
FileEx.SafeDelete(testFilesDir.GetTestPath("Asym_DIA.skyd"));
}
{
// Import with prespecified isolation windows
var windowList = new List <IsolationWindow>
{
new IsolationWindow(999.2702214, 1024.270221),
new IsolationWindow(1024.27267, 1049.27267)
};
SrmDocument docPrespecified = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fullScan =>
fullScan.ChangeAcquisitionMethod(fullScan.AcquisitionMethod, new IsolationScheme("Test prespecified", windowList))));
AssertEx.Serializable(docPrespecified);
Assert.IsTrue(docContainer.SetDocument(docPrespecified, doc, false));
SrmDocument docResults = docContainer.ChangeMeasuredResults(measuredResults, expectedMoleculeCount, 1, 1, 2, 2);
nodeGroup = docResults.MoleculeTransitionGroups.First();
ratio = nodeGroup.Results[0][0].Ratio ?? 0;
// Asymmetric should be a lot closer to 1.0
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.masses_only) // Can't use labels without a formula
{
Assert.AreEqual(fixedRatio, ratio, 0.05);
}
// Revert to original document, and get rid of results cache
Assert.IsTrue(docContainer.SetDocument(doc, docResults, false));
FileEx.SafeDelete(testFilesDir.GetTestPath("Asym_DIA.skyd"));
}
{
// Import with prespecified targets
var windowList = new List <IsolationWindow>
{
new IsolationWindow(999.2702214, 1024.270221, 1004.27),
new IsolationWindow(1024.27267, 1049.27267, 1029.27)
};
SrmDocument docPrespecified = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fullScan =>
fullScan.ChangeAcquisitionMethod(fullScan.AcquisitionMethod, new IsolationScheme("Test target", windowList))));
AssertEx.Serializable(docPrespecified);
Assert.IsTrue(docContainer.SetDocument(docPrespecified, doc, false));
SrmDocument docResults = docContainer.ChangeMeasuredResults(measuredResults, expectedMoleculeCount, 1, 1, 2, 2);
nodeGroup = docResults.MoleculeTransitionGroups.First();
ratio = nodeGroup.Results[0][0].Ratio ?? 0;
// Asymmetric should be a lot closer to 1.0
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.masses_only) // Can't use labels without a formula
{
Assert.AreEqual(fixedRatio, ratio, 0.05);
}
// Revert to original document, and get rid of results cache
Assert.IsTrue(docContainer.SetDocument(doc, docResults, false));
FileEx.SafeDelete(testFilesDir.GetTestPath("Asym_DIA.skyd"));
}
{
// Import with ambiguous prespecified targets
var windowList = new List <IsolationWindow>
{
new IsolationWindow(999.2702214, 1024.270221, 1004.27),
new IsolationWindow(1000.0, 1049.27267, 1004.28)
};
SrmDocument docAmbiguous = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fullScan =>
fullScan.ChangeAcquisitionMethod(fullScan.AcquisitionMethod, new IsolationScheme("Test ambiguous", windowList))));
AssertEx.Serializable(docAmbiguous);
Assert.IsTrue(docContainer.SetDocument(docAmbiguous, doc, false));
try
{
docContainer.ChangeMeasuredResults(measuredResults, expectedMoleculeCount, 1, 1, 2, 2);
Assert.Fail("Expected ambiguous isolation targets.");
}
catch (Exception x)
{
AssertEx.AreComparableStrings(Resources.SpectrumFilter_FindFilterPairs_Two_isolation_windows_contain_targets_which_match_the_isolation_target__0__, x.Message, 1);
}
// Revert to original document, and get rid of results cache
Assert.IsTrue(docContainer.SetDocument(doc, docContainer.Document, false));
FileEx.SafeDelete(testFilesDir.GetTestPath("Asym_DIA.skyd"));
}
{
// Import with one isolation window, so one result is discarded.
var windowList = new List <IsolationWindow>
{
new IsolationWindow(999.2702214, 1024.270221),
};
SrmDocument docOneWindow = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fullScan =>
fullScan.ChangeAcquisitionMethod(fullScan.AcquisitionMethod, new IsolationScheme("Test one window", windowList))));
AssertEx.Serializable(docOneWindow);
Assert.IsTrue(docContainer.SetDocument(docOneWindow, doc, false));
SrmDocument docResults = docContainer.ChangeMeasuredResults(measuredResults, 1, 1, 0, 2, 0);
nodeGroup = docResults.MoleculeTransitionGroups.First();
Assert.IsNull(nodeGroup.Results[0][0].Ratio);
// Revert to original document, and get rid of results cache
Assert.IsTrue(docContainer.SetDocument(doc, docResults, false));
FileEx.SafeDelete(testFilesDir.GetTestPath("Asym_DIA.skyd"));
}
}
testFilesDir.Dispose();
}
