public void cannotFindMassTag_test1()
{
//
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var run = RunUtilities.CreateAndAlignRun(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 26523;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 1 select n).First();
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
var workflow = new BasicTargetedWorkflow(run, parameters);
workflow.Execute();
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag) as MassTagResult;
Assert.IsNull(result.IsotopicProfile);
Assert.IsNull(result.ScanSet);
Assert.IsNull(result.ChromPeakSelected);
Assert.IsTrue(result.FailedResult);
Assert.AreEqual(DeconTools.Backend.Globals.TargetedResultFailureType.ChrompeakNotFoundWithinTolerances, result.FailureType);
}
public List <MassTagResultBase> FindTargetsThatPassCriteria()
{
Check.Require(this.MassTagList != null && this.MassTagList.Count > 0, "MassTags have not been defined.");
Check.Require(_run != null, "Run is null");
List <MassTagResultBase> resultsPassingCriteria = new List <MassTagResultBase>();
int netGroupingCounter = 0;
foreach (var netGrouping in _netGroupings)
{
string progressString = "NET grouping " + netGrouping.Lower;
reportProgess(progressString);
netGroupingCounter++;
var filteredMasstags = (from n in this.MassTagList
where n.NETVal >= netGrouping.Lower && n.NETVal < netGrouping.Upper
select n);
int numPassingMassTagsInGrouping = 0;
int numFailingMassTagsInGrouping = 0;
foreach (var massTag in filteredMasstags)
{
_run.CurrentMassTag = massTag;
_workflow.Execute();
var result = _run.ResultCollection.GetMassTagResult(massTag);
if (resultPassesCriteria(result))
{
reportProgess(massTag.ID + "; z= " + massTag.ChargeState + " added.");
resultsPassingCriteria.Add(result); //where passing results are added
numPassingMassTagsInGrouping++;
}
else
{
numFailingMassTagsInGrouping++;
}
if (numPassingMassTagsInGrouping >= NumberOfDesiredMassTagsFoundPerNETGrouping)
{
break; //found enough massTags in this grouping
}
if (numFailingMassTagsInGrouping > NumberOfMaxAttemptsPerNETGrouping)
{
break; // too many failed massTags in this grouping. Will move on to next grouping
}
}
}
return(resultsPassingCriteria);
}
public void findFeatureIn_dataset_with_bad_massCalibration_test1()
{
//mass error in this dataset is typically ~50ppm.
var datasetFile = @"D:\Data\Orbitrap\Subissue01\QC_Shew_10_01-pt5-1_8Feb10_Doc_09-12-24.RAW";
var massTagFile = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\MassTags\QCShew_Formic_MassTags_Bin10_first10.txt";
var workflowParameterFile = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\WorkflowParameterFiles\UnlabelledTargeted_WorkflowParameters_noSum.xml";
var run = RunUtilities.CreateAndLoadPeaks(datasetFile, datasetFile.Replace(".RAW", "_peaks.txt"));
RunUtilities.AlignRunUsingAlignmentInfoInFiles(run);
Assert.IsTrue(run.MassIsAligned);
Assert.IsTrue(run.NETIsAligned);
var parameters = new BasicTargetedWorkflowParameters();
parameters.LoadParameters(workflowParameterFile);
var workflow = new BasicTargetedWorkflow(parameters);
workflow.Run = run;
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var mt1 = (from n in mtc.TargetList where n.ID == 24702 && n.ChargeState == 4 select n).First();
run.CurrentMassTag = mt1;
workflow.Execute();
var repo = new TargetedResultRepository();
repo.AddResult(workflow.Result);
Console.WriteLine("theor mono mass = " + mt1.MonoIsotopicMass);
Console.WriteLine("theorMZ = " + mt1.MZ);
Console.WriteLine("theorNET = " + mt1.NormalizedElutionTime);
Console.WriteLine("obsScan = " + repo.Results[0].ScanLC);
Console.WriteLine("obsNET = " + repo.Results[0].NET);
Console.WriteLine("NETError = " + repo.Results[0].NETError);
Console.WriteLine("obsMZ = " + repo.Results[0].MonoMZ);
Console.WriteLine("monoMass = " + repo.Results[0].MonoMass);
Console.WriteLine("obsMonoMassCalibrated = " + repo.Results[0].MonoMassCalibrated);
Console.WriteLine("MassErrorBeforeAlignment = " + (mt1.MZ - repo.Results[0].MonoMZ) / mt1.MZ * 1e6);
Console.WriteLine("MassErrorAfterAlignment = " + repo.Results[0].MassErrorBeforeCalibration);
}
public void exporterTest1()
{
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_NETVals0.3-0.33.txt";
var exportedResultFile = Path.Combine(FileRefs.OutputFolderPath, "UnlabelledTargetedResultsExporterOutput1.txt");
if (File.Exists(exportedResultFile))
{
File.Delete(exportedResultFile);
}
var run = RunUtilities.CreateAndAlignRun(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var selectedMassTags = mtc.TargetList.OrderBy(p => p.ID).Take(10).ToList();
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
var workflow = new BasicTargetedWorkflow(run, parameters);
foreach (var mt in selectedMassTags)
{
run.CurrentMassTag = mt;
workflow.Execute();
}
var repo = new TargetedResultRepository();
repo.AddResults(run.ResultCollection.GetMassTagResults());
var exporter = new UnlabelledTargetedResultToTextExporter(exportedResultFile);
exporter.ExportResults(repo.Results);
}
public void findSingleMassTag_checkAlignmentData_test1()
{
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var run = RunUtilities.CreateAndLoadPeaks(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 24800;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
var workflow = new BasicTargetedWorkflow(run, parameters);
workflow.Execute();
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag) as MassTagResult;
Assert.AreEqual(false, result.FailedResult);
result.DisplayToConsole();
Assert.IsNotNull(result.IsotopicProfile);
Assert.IsNotNull(result.ScanSet);
Assert.IsNotNull(result.ChromPeakSelected);
Assert.AreEqual(2, result.IsotopicProfile.ChargeState);
Assert.AreEqual(718.41m, (decimal)Math.Round(result.IsotopicProfile.GetMZ(), 2));
Assert.AreEqual(5947m, (decimal)Math.Round(result.ChromPeakSelected.XValue));
Assert.AreEqual(5.91, (decimal)(Math.Round(result.GetMassErrorAfterAlignmentInPPM(), 2)));
Assert.AreEqual(0.0001585m, (decimal)(Math.Round(result.GetNETAlignmentError(), 7)));
RunUtilities.AlignRunUsingAlignmentInfoInFiles(run);
//these might change due to unit tests elsewhere. Need a better way of doing this
//Assert.AreEqual(1.99290383722318m, (decimal)result.GetMassErrorAfterAlignmentInPPM());
//Assert.AreEqual(0.00076708197593689m, (decimal)result.GetNETAlignmentError());
}
public void findSingleModifiedMassTagTest1()
{
var testFile = UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_NETVals0.3-0.33.txt";
var run = RunUtilities.CreateAndLoadPeaks(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 189685150;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();
Assert.AreEqual(true, run.CurrentMassTag.ContainsMods);
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromatogramCorrelationIsPerformed = true;
var workflow = new BasicTargetedWorkflow(run, parameters);
workflow.Execute();
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag) as MassTagResult;
Assert.AreEqual(false, result.FailedResult);
result.DisplayToConsole();
Assert.IsNotNull(result.IsotopicProfile);
Assert.IsNotNull(result.ScanSet);
Assert.IsNotNull(result.ChromPeakSelected);
Assert.AreEqual(2, result.IsotopicProfile.ChargeState);
Assert.AreEqual(959.48m, (decimal)Math.Round(result.IsotopicProfile.GetMZ(), 2));
//Assert.AreEqual(6070, (decimal)Math.Round(result.ChromPeakSelected.XValue));
foreach (var dataItem in result.ChromCorrelationData.CorrelationDataItems)
{
Console.WriteLine(dataItem);
}
}
public void ensure_alignmentIsBeingUsed_duringProcessing_test2()
{
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var mzAlignmentInfoFilename = @"D:\Data\Orbitrap\QC_Shew_08_04-pt1-3_15Apr09_Sphinx_09-02-16_MZAlignment.txt";
var NETAlignmentInfoFilename = @"D:\Data\Orbitrap\QC_Shew_08_04-pt1-3_15Apr09_Sphinx_09-02-16_NETAlignment.txt";
var rawDataFile = @"D:\Data\Orbitrap\QC_Shew_08_04-pt1-3_15Apr09_Sphinx_09-02-16.RAW";
var peaksDataFile = @"D:\Data\Orbitrap\QC_Shew_08_04-pt1-3_15Apr09_Sphinx_09-02-16_peaks.txt";
var run = DeconTools.Backend.Utilities.RunUtilities.CreateAndLoadPeaks(rawDataFile, peaksDataFile);
var importer = new MassAlignmentInfoFromTextImporter(mzAlignmentInfoFilename);
var massAlignmentData = importer.Import();
var massAlignmentInfo = new MassAlignmentInfoLcmsWarp();
massAlignmentInfo.SetMassAlignmentData(massAlignmentData);
run.MassAlignmentInfo = massAlignmentInfo;
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 24730;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();
//first will execute workflow on a dataset that was NOT aligned
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromNETTolerance = 0.2; //use a very wide tolerance
parameters.ChromGenTolerance = 5;
parameters.MSToleranceInPPM = 15;
var workflow = new BasicTargetedWorkflow(run, parameters);
workflow.Execute();
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag);
Assert.IsTrue(result.ChromPeakSelected != null);
Assert.AreEqual(9367, (int)result.ChromPeakSelected.XValue);
var netDiff = result.Target.NormalizedElutionTime - result.GetNET();
Console.WriteLine("NET diff before alignment = " + netDiff);
var expectedNETDiff = 0.071m;
Assert.AreEqual(expectedNETDiff, (decimal)Math.Round(netDiff, 3));
//import NET alignment information
var netAlignmentInfoImporter = new NETAlignmentFromTextImporter(NETAlignmentInfoFilename);
var scanNETdata = netAlignmentInfoImporter.Import();
run.NetAlignmentInfo.SetScanToNETAlignmentData(scanNETdata);
parameters = new BasicTargetedWorkflowParameters();
parameters.ChromNETTolerance = 0.01; //use a more narrow tolerance
parameters.ChromGenTolerance = 5;
parameters.MSToleranceInPPM = 15;
workflow = new BasicTargetedWorkflow(run, parameters);
workflow.Execute();
netDiff = result.Target.NormalizedElutionTime - result.GetNET();
Console.WriteLine("NET diff after alignment = " + netDiff);
Assert.IsTrue(result.ChromPeakSelected != null);
var expectedNETDiffMaximum = 0.01;
Assert.IsTrue(netDiff < expectedNETDiffMaximum);
}
public void findSingleMassTag_test1()
{
//see https://jira.pnnl.gov/jira/browse/OMCS-709
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var run = RunUtilities.CreateAndAlignRun(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 24800;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromatogramCorrelationIsPerformed = true;
parameters.ChromSmootherNumPointsInSmooth = 9;
parameters.ChromPeakDetectorPeakBR = 1;
parameters.ChromPeakDetectorSigNoise = 1;
var workflow = new BasicTargetedWorkflow(run, parameters);
workflow.Execute();
Assert.IsNotNull(workflow.ChromatogramXYData, "Chrom XY data is empty");
Assert.IsNotEmpty(workflow.ChromPeaksDetected, "Chrom peaks are empty");
Console.WriteLine("Chrom peaks detected");
foreach (var chromPeak in workflow.ChromPeaksDetected)
{
Console.WriteLine(chromPeak.XValue.ToString("0.0") + "\t" + chromPeak.Height.ToString("0") + "\t" +
chromPeak.Width.ToString("0.0"));
}
Assert.AreEqual(3, workflow.ChromPeaksDetected.Count);
Assert.IsNotNull(workflow.ChromPeakSelected, "No chrom peak was selected");
Assert.IsNotNull(workflow.MassSpectrumXYData, "Mass spectrum for selected chrom peak was not generated");
//TestUtilities.DisplayXYValues(workflow.MassSpectrumXYData);
//TestUtilities.DisplayXYValues(workflow.ChromatogramXYData);
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag) as MassTagResult;
if (result.FailedResult)
{
Console.WriteLine(result.ErrorDescription);
}
Assert.IsFalse(result.FailedResult);
// result.DisplayToConsole();
Assert.IsNotNull(result.IsotopicProfile);
Assert.IsNotNull(result.ScanSet);
Assert.IsNotNull(result.ChromPeakSelected);
Assert.AreEqual(2, result.IsotopicProfile.ChargeState);
Assert.AreEqual(718.41m, (decimal)Math.Round(result.IsotopicProfile.GetMZ(), 2));
Assert.AreEqual(5939, (decimal)Math.Round(result.ChromPeakSelected.XValue));
Assert.IsNotNull(result.ChromCorrelationData);
foreach (var dataItem in result.ChromCorrelationData.CorrelationDataItems)
{
Console.WriteLine(dataItem);
}
}
public void findSingleMassTag_alternateQCShew()
{
var testFile = @"D:\Data\Orbitrap\QC_Shew_08_04-pt1-3_15Apr09_Sphinx_09-02-16.RAW";
var peaksTestFile = @"D:\Data\Orbitrap\QC_Shew_08_04-pt1-3_15Apr09_Sphinx_09-02-16_peaks.txt";
var massTagFile = @"D:\Data\Orbitrap\QC_Shew_08_04-pt1-3_15Apr09_Sphinx_09-02-16_peakMatchedFeatures.txt";
var run = RunUtilities.CreateAndLoadPeaks(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 24709;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 4 select n).First();
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromNETTolerance = 0.2;
parameters.MSToleranceInPPM = 25;
parameters.ChromatogramCorrelationIsPerformed = true;
var workflow = new BasicTargetedWorkflow(run, parameters);
workflow.Execute();
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag) as MassTagResult;
result.DisplayToConsole();
Assert.IsNotNull(result.IsotopicProfile);
Assert.IsNotNull(result.ScanSet);
Assert.IsNotNull(result.ChromPeakSelected);
Assert.AreEqual(4, result.IsotopicProfile.ChargeState);
// Assert.AreEqual(610.81m, (decimal)Math.Round(result.IsotopicProfile.GetMZ(), 2));
//Assert.AreEqual(6483, (decimal)Math.Round(result.ChromPeakSelected.XValue));
double maxIntensity = result.IsotopicProfile.Peaklist.Max(p => p.Height);
for (var i = 0; i < result.IsotopicProfile.Peaklist.Count; i++)
{
double correctedRatio = 0;
if (i < result.ChromCorrelationData.CorrelationDataItems.Count)
{
var correlationSlope = result.ChromCorrelationData.CorrelationDataItems[i].CorrelationSlope;
if (correlationSlope != null)
{
correctedRatio = (double)correlationSlope;
}
}
else
{
correctedRatio = 0;
}
var observedRelIntensity = result.IsotopicProfile.Peaklist[i].Height / maxIntensity;
Console.WriteLine(i + "\t" + observedRelIntensity + "\t" + correctedRatio);
}
}
