public void DoFullScanSettingsTest(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules,
out List <SrmDocument> docCheckPoints)
{
TestSmallMolecules = false; // Don't need that magic extra node, we have an explicit test
docCheckPoints = new List <SrmDocument>();
var doc0 = ResultsUtil.DeserializeDocument("MultiLabel.sky", GetType());
var refine = new RefinementSettings();
var docSM = refine.ConvertToSmallMolecules(doc0, ".", asSmallMolecules);
docCheckPoints.Add(docSM);
Assume.IsFalse(docSM.MoleculeTransitionGroups.Any(nodeGroup => nodeGroup.IsotopeDist != null));
AssertEx.Serializable(docSM, AssertEx.Cloned);
double c13Delta = BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.C13) -
BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.C);
double n15Delta = BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.N15) -
BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.N);
// Verify isotope distributions calculated when MS1 filtering enabled
var enrichments = IsotopeEnrichmentsList.DEFAULT;
var docIsotopes = docSM.ChangeSettings(docSM.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 3, enrichments)));
docCheckPoints.Add(docIsotopes);
Assume.AreEqual(FullScanMassAnalyzerType.tof,
docIsotopes.Settings.TransitionSettings.FullScan.PrecursorMassAnalyzer);
Assume.IsFalse(docIsotopes.MoleculeTransitionGroups.Any(nodeGroup => nodeGroup.IsotopeDist == null));
foreach (var nodeGroup in docIsotopes.MoleculeTransitionGroups)
{
Assume.AreEqual(3, nodeGroup.Children.Count);
var isotopePeaks = nodeGroup.IsotopeDist;
Assume.IsNotNull(isotopePeaks);
Assume.IsTrue(nodeGroup.HasIsotopeDist);
// The peaks should always includ at least M-1
Assume.IsTrue(isotopePeaks.MassIndexToPeakIndex(0) > 0);
// Within 2.5% of 100% of the entire isotope distribution
Assert.AreEqual(1.0, isotopePeaks.ExpectedProportions.Sum(), 0.025);
// Precursor mass and m/z values are expected to match exactly (well, within XML roundtrip accuracy anyway)
Assume.AreEqual(nodeGroup.PrecursorMz, nodeGroup.IsotopeDist.GetMZI(0), SequenceMassCalc.MassTolerance);
Assume.AreEqual(nodeGroup.PrecursorMz, nodeGroup.TransitionGroup.IsCustomIon ?
BioMassCalc.CalculateIonMz(nodeGroup.IsotopeDist.GetMassI(0),
nodeGroup.TransitionGroup.PrecursorAdduct.Unlabeled) :
SequenceMassCalc.GetMZ(nodeGroup.IsotopeDist.GetMassI(0),
nodeGroup.TransitionGroup.PrecursorAdduct), SequenceMassCalc.MassTolerance);
// Check isotope distribution masses
for (int i = 1; i < isotopePeaks.CountPeaks; i++)
{
int massIndex = isotopePeaks.PeakIndexToMassIndex(i);
Assume.IsTrue(isotopePeaks.GetMZI(massIndex - 1) < isotopePeaks.GetMZI(massIndex));
double massDelta = GetMassDelta(isotopePeaks, massIndex);
if (nodeGroup.TransitionGroup.LabelType.IsLight)
{
// All positive should be close to 13C - C, and 0 should be the same as the next delta
double expectedDelta = (massIndex > 0 ? c13Delta : GetMassDelta(isotopePeaks, massIndex + 1));
Assume.AreEqual(expectedDelta, massDelta, 0.001);
}
else if (nodeGroup.TransitionGroup.LabelType.Name.Contains("15N"))
{
// All positive should be close to 13C, and all negative 15N
double expectedDelta = (massIndex > 0 ? c13Delta : n15Delta);
Assume.AreEqual(expectedDelta, massDelta, 0.0015);
}
else if (massIndex == 0)
{
double expectedDelta = (isotopePeaks.GetProportionI(massIndex - 1) == 0
? GetMassDelta(isotopePeaks, massIndex + 1)
: 1.0017);
Assume.AreEqual(expectedDelta, massDelta, 0.001);
}
else
{
Assume.AreEqual(c13Delta, massDelta, 0.001);
}
}
}
AssertEx.Serializable(docIsotopes, AssertEx.Cloned);
// Narrow the resolution, and verify that predicted proportion of the isotope
// distribution captured is reduced for all precursors
var docIsotopesFt = docIsotopes.ChangeSettings(docIsotopes.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorResolution(FullScanMassAnalyzerType.ft_icr, 500 * 1000, 400)));
docCheckPoints.Add(docIsotopesFt);
var tranGroupsOld = docIsotopes.MoleculeTransitionGroups.ToArray();
var tranGroupsNew = docIsotopesFt.MoleculeTransitionGroups.ToArray();
Assume.AreEqual(tranGroupsOld.Length, tranGroupsNew.Length);
for (int i = 0; i < tranGroupsOld.Length; i++)
{
Assert.AreNotSame(tranGroupsOld[i], tranGroupsNew[i]);
Assert.AreNotSame(tranGroupsOld[i].IsotopeDist, tranGroupsNew[i].IsotopeDist);
Assume.IsTrue(tranGroupsOld[i].IsotopeDist.ExpectedProportions.Sum() >
tranGroupsNew[i].IsotopeDist.ExpectedProportions.Sum());
}
// Use Min % of base peak and verify variation in transitions used
const float minPercent1 = 10;
var docIsotopesP1 = docIsotopes.ChangeSettings(docIsotopes.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Percent, minPercent1, enrichments)));
docCheckPoints.Add(docIsotopesP1);
tranGroupsNew = docIsotopesP1.MoleculeTransitionGroups.ToArray();
int maxTran = 0;
for (int i = 0; i < tranGroupsOld.Length; i++)
{
// Isotope distributions should not have changed
var isotopePeaks = tranGroupsNew[i].IsotopeDist;
Assert.AreSame(tranGroupsOld[i].IsotopeDist, isotopePeaks);
// Expected transitions should be present
maxTran = Math.Max(maxTran, tranGroupsNew[i].Children.Count);
foreach (TransitionDocNode nodeTran in tranGroupsNew[i].Children)
{
int massIndex = nodeTran.Transition.MassIndex;
Assume.IsTrue(minPercent1 <= isotopePeaks.GetProportionI(massIndex) * 100.0 / isotopePeaks.BaseMassPercent);
}
}
Assume.AreEqual(5, maxTran);
AssertEx.Serializable(docIsotopesP1, AssertEx.Cloned); // Express any failure in terms of XML diffs
// Use 10%, and check that 15N modifications all have M-1
const float minPercent2 = 5;
var docIsotopesP2 = docIsotopesP1.ChangeSettings(docIsotopesP1.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Percent, minPercent2, enrichments)));
docCheckPoints.Add(docIsotopesP2);
foreach (var nodeGroup in docIsotopesP2.MoleculeTransitionGroups)
{
var firstChild = (TransitionDocNode)nodeGroup.Children[0];
if (nodeGroup.TransitionGroup.LabelType.Name.EndsWith("15N"))
{
Assume.AreEqual(-1, firstChild.Transition.MassIndex);
}
else
{
Assume.AreNotEqual(-1, firstChild.Transition.MassIndex);
}
}
AssertEx.Serializable(docIsotopesP2, AssertEx.Cloned);
// Use lower enrichment of 13C, and verify that this add M-1 for 13C labeled precursors
var enrichmentsLow13C = enrichments.ChangeEnrichment(new IsotopeEnrichmentItem(BioMassCalc.C13, 0.9));
var docIsotopesLow13C = docIsotopesP1.ChangeSettings(docIsotopesP1.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Percent, minPercent2, enrichmentsLow13C)));
tranGroupsNew = docIsotopesLow13C.MoleculeTransitionGroups.ToArray();
for (int i = 0; i < tranGroupsOld.Length; i++)
{
var nodeGroup = tranGroupsNew[i];
if (!Equals(nodeGroup.TransitionGroup.LabelType.Name, "heavy"))
{
Assert.AreSame(tranGroupsOld[i].IsotopeDist, nodeGroup.IsotopeDist);
}
else
{
var firstChild = (TransitionDocNode)nodeGroup.Children[0];
Assume.IsTrue(firstChild.Transition.MassIndex < 0);
}
}
AssertEx.Serializable(docIsotopesLow13C, AssertEx.Cloned); // Express any failure as XML diffs
// Use 0%, and check that everything has M-1 and lower
var enrichmentsLow = enrichmentsLow13C.ChangeEnrichment(new IsotopeEnrichmentItem(BioMassCalc.N15, 0.97));
var docIsotopesLowP0 = docIsotopesP1.ChangeSettings(docIsotopesP1.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Percent, 0, enrichmentsLow)));
docCheckPoints.Add(docIsotopesLowP0);
foreach (var nodeGroup in docIsotopesLowP0.MoleculeTransitionGroups)
{
Assume.AreEqual(nodeGroup.IsotopeDist.CountPeaks, nodeGroup.Children.Count);
var firstChild = (TransitionDocNode)nodeGroup.Children[0];
if (nodeGroup.TransitionGroup.LabelType.IsLight)
{
Assume.AreEqual(-1, firstChild.Transition.MassIndex);
}
else
{
Assume.IsTrue(-1 > firstChild.Transition.MassIndex);
}
}
AssertEx.Serializable(docIsotopesLowP0, AssertEx.Cloned);
// Test a document with variable and heavy modifications, which caused problems for
// the original implementation
var docVariable = ResultsUtil.DeserializeDocument("HeavyVariable.sky", GetType());
Assume.IsFalse(docVariable.MoleculeTransitionGroups.Any(nodeGroup => nodeGroup.IsotopeDist == null));
foreach (var nodeGroup in docVariable.MoleculeTransitionGroups)
{
var isotopePeaks = nodeGroup.IsotopeDist;
Assume.IsNotNull(isotopePeaks);
// The peaks should always includ at least M-1
Assume.IsTrue(isotopePeaks.MassIndexToPeakIndex(0) > 0);
// Precursor mass and m/z values are expected to match exactly (well, within XML roundtrip tolerance anyway)
var mzI = nodeGroup.IsotopeDist.GetMZI(0);
Assume.AreEqual(nodeGroup.PrecursorMz, mzI, SequenceMassCalc.MassTolerance);
// Check isotope distribution masses
for (int i = 1; i < isotopePeaks.CountPeaks; i++)
{
int massIndex = isotopePeaks.PeakIndexToMassIndex(i);
Assume.IsTrue(isotopePeaks.GetMZI(massIndex - 1) < isotopePeaks.GetMZI(massIndex));
double massDelta = GetMassDelta(isotopePeaks, massIndex);
bool containsSulfur = nodeGroup.TransitionGroup.Peptide.IsCustomMolecule
? (nodeGroup.CustomMolecule.Formula.IndexOfAny("S".ToCharArray()) != -1)
: (nodeGroup.TransitionGroup.Peptide.Sequence.IndexOfAny("CM".ToCharArray()) != -1);
if (massIndex == 0)
{
double expectedDelta = (isotopePeaks.GetProportionI(massIndex - 1) == 0
? GetMassDelta(isotopePeaks, massIndex + 1)
: 1.0017);
Assume.AreEqual(expectedDelta, massDelta, 0.001);
}
else if (!containsSulfur || massIndex == 1)
{
Assume.AreEqual(c13Delta, massDelta, 0.001);
}
else
{
Assume.AreEqual(1.00075, massDelta, 0.001);
}
}
}
docCheckPoints.Add(docVariable);
}
private void DoFullScanFilterTest(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules,
out List <SrmDocument> docCheckpoints, bool centroided = false)
{
docCheckpoints = new List <SrmDocument>();
TestSmallMolecules = false; // We test small molecules explicitly
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, null, true) }),
};
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 SpectrumPeakAnnotation(CustomIon ion, string comment)
{
Ion = ion ?? CustomIon.EMPTY;
Comment = comment ?? string.Empty;
Assume.IsFalse(IsNullOrEmpty(this), @"empty peak annotation"); // You should be using Create() if there's any risk of creating empty objects
}
public static CustomMolecule FromSmallMoleculeLibraryAttributes(SmallMoleculeLibraryAttributes libraryAttributes)
{
Assume.IsFalse(libraryAttributes.IsEmpty);
SmallMoleculeLibraryAttributes.ParseMolecularFormulaOrMassesString(libraryAttributes.ChemicalFormulaOrMassesString, out var formula, out var monoMass, out var averageMass);
return(new CustomMolecule(formula, monoMass, averageMass, libraryAttributes.MoleculeName, libraryAttributes.CreateMoleculeID()));
}
public CustomMolecule(SmallMoleculeLibraryAttributes libraryAttributes)
: this(libraryAttributes.ChemicalFormula, libraryAttributes.MoleculeName, libraryAttributes.CreateMoleculeID())
{
Assume.IsFalse(libraryAttributes.IsEmpty);
}
public void Start()
{
Assume.IsFalse(_thread.IsAlive); // Called only once
_thread.Start();
}