public void GetPeakChromatogram_IQStyle_Test3()
{
var run = RunUtilities.CreateAndLoadPeaks(FileRefs.RawDataMSFiles.OrbitrapStdFile1, FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
var target = TestUtilities.GetIQTargetStandard(1);
var chromGen = new PeakChromatogramGenerator();
chromGen.ChromatogramGeneratorMode = Globals.ChromatogramGeneratorMode.TOP_N_PEAKS;
chromGen.TopNPeaksLowerCutOff = 0.4;
chromGen.Tolerance = 100;
var lowerScan = 6087;
var upperScan = 6418;
var massOfInterest = new List <double>();
massOfInterest.Add(target.TheorIsotopicProfile.Peaklist[0].XValue);
massOfInterest.Add(target.TheorIsotopicProfile.Peaklist[1].XValue);
var chromXYData = chromGen.GenerateChromatogram(run, massOfInterest, lowerScan, upperScan, chromGen.Tolerance, chromGen.ToleranceUnit);
Assert.IsNotNull(chromXYData);
Assert.AreEqual(96, chromXYData.Xvalues.Length);
TestUtilities.DisplayXYValues(chromXYData);
}
public void GetChromatogramsTest1()
{
string testDatasetPath =
@"D:\Data\From_Vlad\Bruker\2013_01_29_ALZ_CTRL_5_0p5_1_01_228.d";
Run run = RunUtilities.CreateAndLoadPeaks(testDatasetPath);
PeakChromatogramGenerator chromGen = new PeakChromatogramGenerator(10);
double targetMZ = 663.3404;
int chargeState = 2;
int peakNum = 4;
targetMZ = targetMZ + peakNum * Globals.MASS_DIFF_BETWEEN_ISOTOPICPEAKS / chargeState;
double toleranceInPPM = 10;
int startScan = 230;
int stopScan = 300;
chromGen.GenerateChromatogram(run, startScan, stopScan, targetMZ, toleranceInPPM);
run.XYData = run.XYData.TrimData(startScan, stopScan);
TestUtilities.DisplayXYValues(run.XYData);
}
public void Get3DElutionAndExportToFileTest1()
{
var peaksFile = FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var orbiFile = FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var run = RunUtilities.CreateAndLoadPeaks(orbiFile, peaksFile);
var outputFile = Path.Combine(run.DataSetPath, run.DatasetName + "_sample3DelutionProfile.txt");
Assert.IsNotNull(run);
Assert.IsTrue(run.ResultCollection.MSPeakResultList.Count > 0);
var extractor = new IsotopicProfileElutionExtractor();
var minScan = 5900;
var maxScan = 6300;
double minMZ = 749;
double maxMZ = 754;
int[] scans;
float[] intensities;
double[] mzBinVals;
extractor.Get3DElutionProfileFromPeakLevelData(run, minScan, maxScan, minMZ, maxMZ, out scans, out mzBinVals, out intensities);
var intensities2D = extractor.GetIntensitiesAs2DArray();
extractor.OutputElutionProfileToFile(outputFile);
}
public void TestFindMassTag()
{
const string testFile = @"\\protoapps\UserData\Kaipo\TopDown\test2\Proteus_Peri_intact_ETD.raw";
const string peaksTestFile = @"\\protoapps\UserData\Kaipo\TopDown\test2\Proteus_Peri_intact_ETD_peaks.txt";
const string massTagFile = @"\\protoapps\UserData\Kaipo\TopDown\test2\Proteus_Peri_intact_ETD_MSAlign_ResultTable.txt";
Run run = RunUtilities.CreateAndLoadPeaks(testFile, peaksTestFile);
TargetCollection mtc = new TargetCollection();
var mtimporter = new MassTagFromMSAlignFileImporter(massTagFile);
mtc = mtimporter.Import();
const int testMassTagID = 14;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID select n).First();
TargetedWorkflowParameters parameters = new TopDownTargetedWorkflowParameters();
var workflow = new TopDownTargetedWorkflow(run, parameters);
workflow.Execute();
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag);
if (result.FailedResult)
{
Console.WriteLine(result.ErrorDescription);
}
Assert.IsFalse(result.FailedResult);
result.DisplayToConsole();
}
public void featuresFoundByTargetedProcessing_thenAligned_test1()
{
string peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile1;
Console.WriteLine("loading peaks.");
Run run = RunUtilities.CreateAndLoadPeaks(FileRefs.RawDataMSFiles.OrbitrapStdFile1, peaksTestFile);
Console.WriteLine("done.");
string massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt";
DeconToolsTargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromNETTolerance = 0.2;
parameters.ChromToleranceInPPM = 25;
parameters.ChromGeneratorMode = Backend.ProcessingTasks.ChromatogramGeneratorMode.MOST_ABUNDANT_PEAK;
parameters.ChromPeakDetectorPeakBR = 2;
parameters.ChromPeakDetectorSigNoise = 2;
parameters.MSToleranceInPPM = 25;
TargetedAligner aligner = new TargetedAligner(run, parameters);
aligner.UpperFitScoreAllowedCriteria = 0.1;
aligner.IScoreAllowedCriteria = 0.15;
Console.WriteLine("Loading Mass tags...");
aligner.SetMassTags(massTagFile);
Console.WriteLine("Done.");
aligner.Execute();
}
public void Get3DElutionTest1()
{
var peaksFile = FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var orbiFile = FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var run = RunUtilities.CreateAndLoadPeaks(orbiFile, peaksFile);
Assert.IsNotNull(run);
Assert.IsTrue(run.ResultCollection.MSPeakResultList.Count > 0);
var extractor = new IsotopicProfileElutionExtractor();
var minScan = 5900;
var maxScan = 6300;
double minMZ = 749;
double maxMZ = 754;
int[] scans;
float[] intensities;
double[] mzBinVals;
extractor.Get3DElutionProfileFromPeakLevelData(run, minScan, maxScan, minMZ, maxMZ, out scans, out mzBinVals, out intensities);
var intensities2D = extractor.GetIntensitiesAs2DArray();
Console.WriteLine(extractor.OutputElutionProfileAsString());
}
public void standardQCShewDatasetTest1()
{
var datasetFile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
var massTagFile = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\MassTags\QCShew_Formic_MassTags_for_alignment.txt";
var workflowParameterFile = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\WorkflowParameterFiles\TargetedAlignmentWorkflowParameters1.xml";
var run = RunUtilities.CreateAndLoadPeaks(datasetFile, datasetFile.Replace(".RAW", "_peaks.txt"));
var parameters = new TargetedAlignerWorkflowParameters();
parameters.LoadParameters(workflowParameterFile);
parameters.ChromNETTolerance = 0.3;
parameters.ChromGenTolerance = 60;
parameters.MSToleranceInPPM = 60;
Console.WriteLine(parameters.ToStringWithDetails());
var aligner = new TargetedAlignerWorkflow(run, parameters);
aligner.outputToConsole = true;
aligner.SetMassTags(massTagFile);
aligner.Execute();
}
public void FailureToFindAnyChromatogramDataTest1()
{
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);
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromGenTolerance = 1; //very narrow tolerance
IqWorkflow iqWorkflow = new BasicIqWorkflow(run, parameters);
IqTarget target = new IqChargeStateTarget(iqWorkflow);
target.EmpiricalFormula = DeconTools.Backend.Utilities.IsotopeDistributionCalculation.IsotopicDistributionCalculator.Instance.GetAveragineFormulaAsString(1399);
target.ElutionTimeTheor = 0.3;
target.ChargeState = 1;
target.DoWorkflow();
var result = target.GetResult();
Assert.IsTrue(result.Target.TheorIsotopicProfile != null);
Assert.IsTrue(result != null);
Assert.IsTrue(result.IqResultDetail.Chromatogram == null);
var reportString = result.ToStringWithDetailedReport();
Console.WriteLine(reportString);
}
public void problemVladDatasetTest1()
{
var datasetFile =
@"\\protoapps\UserData\Slysz\Data\O16O18\Vlad_O16O18\RawData\test.RAW";
var massTagFile =
@"\\protoapps\UserData\Slysz\Data\O16O18\Vlad_O16O18\Targets\massTags_found_across_all_5_datasets.txt";
var workflowParameterFile =
@"\\protoapps\UserData\Slysz\Data\O16O18\Vlad_O16O18\Workflow_Parameters\TargetedAlignmentWorkflowParameters1.xml";
var run = RunUtilities.CreateAndLoadPeaks(datasetFile, datasetFile.Replace(".RAW", "_peaks.txt"));
var parameters = new TargetedAlignerWorkflowParameters();
parameters.LoadParameters(workflowParameterFile);
parameters.ChromNETTolerance = 0.3;
parameters.ChromGenTolerance = 60;
parameters.MSToleranceInPPM = 60;
Console.WriteLine(parameters.ToStringWithDetails());
var aligner = new TargetedAlignerWorkflow(run, parameters);
aligner.outputToConsole = true;
aligner.SetMassTags(massTagFile);
aligner.Execute();
}
public void featuresFoundByTargetedProcessing_thenAligned_test1()
{
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile1;
var run = RunUtilities.CreateAndLoadPeaks(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1, peaksTestFile);
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_NETVals0.3-0.33.txt";
var parameters = new TargetedAlignerWorkflowParameters();
parameters.ChromNETTolerance = 0.2;
parameters.ChromGenTolerance = 25;
parameters.ChromGeneratorMode = Globals.ChromatogramGeneratorMode.MOST_ABUNDANT_PEAK;
parameters.ChromPeakDetectorPeakBR = 2;
parameters.ChromPeakDetectorSigNoise = 2;
parameters.MSToleranceInPPM = 25;
parameters.UpperFitScoreAllowedCriteria = 0.1;
parameters.IScoreAllowedCriteria = 0.15;
var aligner = new TargetedAlignerWorkflow(run, parameters);
aligner.SetMassTags(massTagFile);
aligner.Execute();
Console.WriteLine(aligner.GetAlignmentReport1());
Assert.IsNotNull(run.AlignmentInfo);
Assert.AreEqual(-4.2m, (decimal)(Math.Round(run.AlignmentInfo.GetPPMShiftFromMZ(600.0f), 1)));
}
public void getPeakChromatogramTest1()
{
var run = RunUtilities.CreateAndLoadPeaks(FileRefs.RawDataMSFiles.OrbitrapStdFile1,
FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
var targetMZ = 759.4032;
var startScan = 5500;
var stopScan = 6500;
double toleranceInPPM = 20;
var chromGen = new PeakChromatogramGenerator();
var mt = TestUtilities.GetMassTagStandard(1);
run.CurrentMassTag = mt;
var unlabelledTheorGenerator = new JoshTheorFeatureGenerator();
unlabelledTheorGenerator.GenerateTheorFeature(mt);
var peakChromGen = new PeakChromatogramGenerator(toleranceInPPM);
peakChromGen.Execute(run.ResultCollection);
run.XYData.Display();
Assert.AreEqual(133, run.XYData.Xvalues.Length);
Assert.AreEqual(5543, (int)run.XYData.Xvalues[35]);
Assert.AreEqual(7319569, (int)run.XYData.Yvalues[35]);
//make sure that the 0's are not trimmed off
Assert.AreEqual(0, run.XYData.Yvalues[1]);
}
public void Get3DElutionAndExportToFileTest1()
{
var rawFile = @"\\protoapps\UserData\Fujimoto\TopDownPaperData\FINAL_DATA\_004\SBEP_STM_004_02272012_Aragon.raw";
var peaksFile = @"\\protoapps\UserData\Fujimoto\TopDownPaperData\FINAL_DATA\_004\SBEP_STM_004_02272012_Aragon_peaks.txt";
var run = RunUtilities.CreateAndLoadPeaks(rawFile, peaksFile);
//var run = new RunFactory().CreateRun(rawFile);
var outputFile = @"\\protoapps\UserData\Fujimoto\TopDownPaperData\FINAL_DATA\_004\3D_PLOT\3DelutionProfile.txt";
Assert.IsNotNull(run);
Assert.IsTrue(run.ResultCollection.MSPeakResultList.Count > 0);
var extractor = new IsotopicProfileElutionExtractor();
var minScan = 3270;
var maxScan = 3350;
double minMZ = 700;
double maxMZ = 1700;
int[] scans;
float[] intensities;
double[] mzBinVals;
extractor.Get3DElutionProfileFromPeakLevelData(run, minScan, maxScan, minMZ, maxMZ, out scans, out mzBinVals, out intensities);
var intensities2D = extractor.GetIntensitiesAs2DArray();
extractor.OutputElutionProfileToFile(outputFile);
}
public XicAdaptor(string rawPath, string peaksPath)
{
Run run = RunUtilities.CreateAndLoadPeaks(rawPath, peaksPath);
m_run = run;
NetWindow = .02;
MzPpmWindow = 20;
}
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 GetPeakChromatogram_usePPMTolerance_Test1()
{
var run = RunUtilities.CreateAndLoadPeaks(FileRefs.RawDataMSFiles.OrbitrapStdFile1,
FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
var targetMZ = 759.4032;
var startScan = 5500;
var stopScan = 6500;
double toleranceInPPM = 20;
var chromGen = new PeakChromatogramGenerator();
var xydata = chromGen.GenerateChromatogram(run, startScan, stopScan, targetMZ, toleranceInPPM, Globals.ToleranceUnit.PPM);
Assert.IsNotNull(xydata);
TestUtilities.DisplayXYValues(xydata);
}
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 findSingleMassTag_test1()
{
var testFile = @"D:\Data\O16O18\Weijun\TechTest_O18_02\TechTest_O18_02_RunA_10Dec09_Doc_09-11-08.RAW";
var massTagFile = @"C:\Users\d3x720\Documents\PNNL\My_DataAnalysis\2011\O16O18_TargetedProcessing\Targets\MassTags_MousePlasma_1709_allChargeStates_nonRedundant.txt";
var peakTestFile = testFile.Replace(".RAW", "_peaks.txt");
var run = RunUtilities.CreateAndLoadPeaks(testFile, peakTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 6643962;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();
TargetedWorkflowParameters parameters = new O16O18WorkflowParameters();
parameters.ChromNETTolerance = 0.1;
parameters.MSToleranceInPPM = 10;
var workflow = new O16O18Workflow(run, parameters);
workflow.Execute();
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag);
Assert.IsNotNull(result);
result.DisplayToConsole();
Assert.IsNotNull(result.IsotopicProfile);
Assert.IsNotNull(result.ScanSet);
Assert.IsNotNull(result.ChromPeakSelected);
Assert.AreEqual(2, result.IsotopicProfile.ChargeState);
Assert.AreEqual(6865, result.ScanSet.PrimaryScanNumber);
}
public void Test1()
{
var testFile = @"\\protoapps\UserData\Slysz\Data\O16O18\BSA\BSA_18O_99_8Jan11_Falcon_10-12-09.RAW";
var massTagFile =
@"\\protoapps\UserData\Slysz\Data\O16O18\BSA\Targets\BSAmassTags_MinimalInfo_withScans.txt";
var peakTestFile = testFile.Replace(".RAW", "_peaks.txt");
var run = RunUtilities.CreateAndLoadPeaks(testFile, peakTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 3;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();
TargetedWorkflowParameters parameters = new O16O18WorkflowParameters();
parameters.ChromNETTolerance = 0.2;
parameters.MSToleranceInPPM = 10;
parameters.ChromPeakSelectorMode = Globals.PeakSelectorMode.MostIntense;
parameters.ChromGeneratorMode = DeconTools.Backend.Globals.ChromatogramGeneratorMode.O16O18_THREE_MONOPEAKS;
parameters.ChromSmootherNumPointsInSmooth = 31;
var workflow = new O16O18Workflow(run, parameters);
workflow.Execute();
Assert.IsTrue(workflow.Result.Target.ScanLCTarget > 0);
Assert.IsNotNull(workflow.ChromPeakSelected);
Assert.AreEqual(10622, (int)workflow.ChromPeakSelected.XValue);
Console.WriteLine("ChromPeak scan value = " + workflow.ChromPeakSelected.XValue);
}
public void GetPeakChromatogram_IQStyle_Test1()
{
var run = RunUtilities.CreateAndLoadPeaks(FileRefs.RawDataMSFiles.OrbitrapStdFile1,
FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
var target = TestUtilities.GetIQTargetStandard(1);
//TestUtilities.DisplayIsotopicProfileData(target.TheorIsotopicProfile);
var chromGen = new PeakChromatogramGenerator();
chromGen.ChromatogramGeneratorMode = Globals.ChromatogramGeneratorMode.TOP_N_PEAKS;
chromGen.TopNPeaksLowerCutOff = 0.4;
chromGen.Tolerance = 10;
var chromXYData = chromGen.GenerateChromatogram(run, target.TheorIsotopicProfile, target.ElutionTimeTheor);
Assert.IsNotNull(chromXYData);
TestUtilities.DisplayXYValues(chromXYData);
}
public void highMassError_DatasetTest1()
{
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_for_alignment.txt";
var workflowParameterFile = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\WorkflowParameterFiles\TargetedAlignmentWorkflowParameters1.xml";
var run = RunUtilities.CreateAndLoadPeaks(datasetFile, datasetFile.Replace(".RAW", "_peaks.txt"));
var parameters = new TargetedAlignerWorkflowParameters();
parameters.LoadParameters(workflowParameterFile);
parameters.ChromNETTolerance = 0.3;
parameters.ChromGenTolerance = 60;
parameters.MSToleranceInPPM = 60;
Console.WriteLine(parameters.ToStringWithDetails());
var aligner = new TargetedAlignerWorkflow(run, parameters);
aligner.outputToConsole = true;
aligner.SetMassTags(massTagFile);
aligner.Execute();
}
public void executeWorkflowTest1()
{
var testFile = FileRefs.SipperRawDataFile;
var exportedResultFile = Path.Combine(FileRefs.OutputFolderPath, "ExportedSipperResults1.txt");
var peaksFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_peaks.txt";
var run = RunUtilities.CreateAndLoadPeaks(testFile, peaksFile);
var lcmsfeaturesFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_LCMSFeatures.txt";
// load LCMSFeatures as targets
var importer =
new LcmsTargetFromFeaturesFileImporter(lcmsfeaturesFile);
var lcmsTargetCollection = importer.Import();
// load MassTags
var massTagFile1 =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_MassTags.txt";
var massTagImporter = new MassTagFromTextFileImporter(massTagFile1);
var massTagCollection = massTagImporter.Import();
//enriched
var testMassTags = new int[] { 355116553, 355129038, 355160150, 355162540, 355163371 };
var filteredLcmsFeatureTargets = (from n in lcmsTargetCollection.TargetList
where testMassTags.Contains(((LcmsFeatureTarget)n).FeatureToMassTagID)
select n).ToList();
TargetCollection.UpdateTargetsWithMassTagInfo(filteredLcmsFeatureTargets, massTagCollection.TargetList);
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromPeakSelectorMode = Globals.PeakSelectorMode.ClosestToTarget;
var workflow = new SipperTargetedWorkflow(run, parameters);
foreach (var target in filteredLcmsFeatureTargets)
{
run.CurrentMassTag = target;
workflow.Execute();
}
var results = run.ResultCollection.GetMassTagResults();
var repo = new TargetedResultRepository();
repo.AddResults(run.ResultCollection.GetMassTagResults());
var exporter = new SipperResultToLcmsFeatureExporter(exportedResultFile);
exporter.ExportResults(repo.Results);
}
public void executeWorkflowTest1()
{
var testFile = FileRefs.SipperRawDataFile;
var peaksFile =
@"C:\Users\d3x720\Documents\PNNL\My_DataAnalysis\2012\C12C13YellowStone\2011_02_20_SIPPER_workflow_standards\Yellow_C13_070_23Mar10_Griffin_10-01-28_peaks.txt";
peaksFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_peaks.txt";
var run = RunUtilities.CreateAndLoadPeaks(testFile, peaksFile);
var lcmsfeaturesFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_LCMSFeatures.txt";
// load LCMSFeatures as targets
var importer =
new LcmsTargetFromFeaturesFileImporter(lcmsfeaturesFile);
var lcmsTargetCollection = importer.Import();
// load MassTags
var massTagFile1 =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_MassTags.txt";
var massTagImporter = new MassTagFromTextFileImporter(massTagFile1);
var massTagCollection = massTagImporter.Import();
var masstagIDlist = (from n in massTagCollection.TargetList select n.ID).ToList();
// Update LCMSFeatures using MassTag info
int[] testMassTags = { 344540889, 344972415, 354881152, 355157363, 355162540, 355315129, 355054192, 355160150 };
//testMassTags = new[] {344540889};
//testMassTags = new int[]
// {
// 354942933, 355066611, 354882356, 354928525, 17440471, 355046165, 355008036, 354977066,
// 355166304, 354879605, 344965520, 354870998, 355084057, 355034961, 354963652, 344969970,
// 355157492, 355176429, 355162540, 355244316, 355139611, 355036935, 355044786, 355139579,
// 355163558, 355065622, 355167968, 355033793, 354879421, 355090391, 355034165, 354880925,
// 344747857, 354879494, 355315129, 344968376, 355022502, 354879347, 354881152, 354879406,
// 344968302, 355037491, 355033717, 355034652, 354879414, 344972415, 355039789, 355025762,
// 355129038, 355355053, 354879164, 355037247, 355033862, 355034180, 355033668, 344540889,
// 355160123, 345073233, 354880183, 354879165, 354879192, 354879842, 355046211, 355033627,
// 355030074, 355033620, 354879142, 354879360, 355034183, 354879174, 354879150
// };
//no enrichment peptides:
//testMassTags = new int[] { 355057553, 355058671, 355084418 };
//enriched
//testMassTags = new int[] { 355116553, 355129038, 355160150, 355162540, 355163371 };
//testMassTags = new int[] { 355008295 };
//co-elution peptides
//testMassTags = new int[] {355034154, 355033668, 355154211, 355035781};
//testMassTags = new int[] { 355033668 };
//testMassTags = new int[]{355157492};
testMassTags = new int[] { 355033977 };
var filteredLcmsFeatureTargets = (from n in lcmsTargetCollection.TargetList
where testMassTags.Contains(((LcmsFeatureTarget)n).FeatureToMassTagID)
select n).ToList();
foreach (LcmsFeatureTarget target in filteredLcmsFeatureTargets)
{
if (masstagIDlist.Contains(target.FeatureToMassTagID))
{
var mt = massTagCollection.TargetList.Where(p => p.ID == target.FeatureToMassTagID).First();
target.Code = mt.Code;
target.EmpiricalFormula = mt.EmpiricalFormula;
}
else
{
//get target's code + empirical formula based on averagine model
}
}
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromPeakSelectorMode = Globals.PeakSelectorMode.ClosestToTarget;
var workflow = new SipperTargetedWorkflow(run, parameters);
var outputFolder = @"C:\data\temp\SipperOutput";
if (!Directory.Exists(outputFolder))
{
Directory.CreateDirectory(outputFolder);
}
var stopwatch = new Stopwatch();
stopwatch.Start();
foreach (var target in filteredLcmsFeatureTargets)
{
run.CurrentMassTag = target;
workflow.Execute();
OutputMassSpectrum(outputFolder, workflow.MassSpectrumXYData, target, workflow.Result as SipperLcmsTargetedResult);
}
stopwatch.Stop();
foreach (var targetedResultBase in (run.ResultCollection.MassTagResultList))
{
var result = (SipperLcmsTargetedResult)targetedResultBase.Value;
Console.WriteLine(result + "\t" + result.Target.IsotopicProfile.Peaklist.Count);
}
Console.WriteLine("Total workflow time (ms) = " + stopwatch.ElapsedMilliseconds);
Console.WriteLine("Time per target (ms) = " + stopwatch.ElapsedMilliseconds / (double)filteredLcmsFeatureTargets.Count);
}
public void GetPeakChromatogram_IQStyle_Test1()
{
//Run run = RunUtilities.CreateAndLoadPeaks(FileRefs.RawDataMSFiles.OrbitrapStdFile1,
// FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
var fileName =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\Orbitrap\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.raw";
var run = RunUtilities.CreateAndLoadPeaks(fileName);
var target = TestUtilities.GetIQTargetStandard(1);
//TestUtilities.DisplayIsotopicProfileData(target.TheorIsotopicProfile);
var chromGen = new PeakChromatogramGenerator();
chromGen.ChromatogramGeneratorMode = Globals.ChromatogramGeneratorMode.TOP_N_PEAKS;
//chromGen.ChromatogramGeneratorMode = Globals.ChromatogramGeneratorMode.;
chromGen.TopNPeaksLowerCutOff = 0.4;
chromGen.Tolerance = 10;
//var chromXYData = chromGen.GenerateChromatogram(run, target.TheorIsotopicProfile, target.ElutionTimeTheor);
// var chromXYData = chromGen.GenerateChromatogram(run, new List<double> { 481.27410, 481.77542, 482.27683 }, 4000, 6500, 0.009, Globals.ToleranceUnit.MZ);
// var chromXYData = chromGen.GenerateChromatogram(run,500,7000,490.26483,0.005,Globals.ToleranceUnit.MZ);
// Assert.IsNotNull(chromXYData);
Console.WriteLine("481.27410");
var chromXYData1 = chromGen.GenerateChromatogram(run, 500, 7000, 481.27410, 0.005, Globals.ToleranceUnit.MZ); TestUtilities.DisplayXYValues(chromXYData1);
// TestUtilities.DisplayXYValues(chromXYData);
var minx1 = chromXYData1.Xvalues.Min();
var maxx1 = chromXYData1.Xvalues.Max();
Console.WriteLine("481.77542");
// chromXYData1.
var chromXYData2 = chromGen.GenerateChromatogram(run, 500, 7000, 481.77542, 0.005, Globals.ToleranceUnit.MZ); TestUtilities.DisplayXYValues(chromXYData2);
// TestUtilities.DisplayXYValues(chromXYData);
var minx2 = chromXYData2.Xvalues.Min();
var maxx2 = chromXYData2.Xvalues.Max();
Console.WriteLine("482.27683");
var chromXYData3 = chromGen.GenerateChromatogram(run, 500, 7000, 482.27683, 0.005, Globals.ToleranceUnit.MZ); TestUtilities.DisplayXYValues(chromXYData3);
TestUtilities.DisplayXYValues(chromXYData3);
var minx3 = chromXYData3.Xvalues.Min();
var maxx3 = chromXYData3.Xvalues.Max();
var minxhelper = Math.Max(minx1, minx2);
var minx = Math.Max(minxhelper, minx3);
var maxxhelper = Math.Min(maxx1, maxx2);
var maxX = Math.Min(maxxhelper, maxx3);
var c1start = chromXYData1.GetClosestXVal(minx);
var c2start = chromXYData2.GetClosestXVal(minx);
var c3start = chromXYData3.GetClosestXVal(minx);
var c1stop = chromXYData1.GetClosestXVal(maxX);
var c2stop = chromXYData2.GetClosestXVal(maxX);
var c3stop = chromXYData3.GetClosestXVal(maxX);
chromXYData1.NormalizeYData();
chromXYData2.NormalizeYData();
chromXYData3.NormalizeYData();
var c1 = new double[c1stop - c1start + 1];
var c2 = new double[c2stop - c2start + 1];
var c3 = new double[c3stop - c3start + 1];
for (int i = c1start, j = 0; i <= c1stop; i++, j++)
{
c1[j] = chromXYData1.Yvalues[i];
}
for (int i = c2start, j = 0; i <= c2stop; i++, j++)
{
c2[j] = chromXYData2.Yvalues[i];
}
for (int i = c3start, j = 0; i <= c3stop; i++, j++)
{
c3[j] = chromXYData3.Yvalues[i];
}
for (var i = 0; i < c1.Length; i++)
{
Console.WriteLine("{0}\t{1}\t{2}", c1[i], c2[i], c3[i]);
}
// double c1chromEven= chromXYData1.Xvalues
var corr1 = MathNet.Numerics.Statistics.Correlation.Pearson(c1, c2);
var corr2 = MathNet.Numerics.Statistics.Correlation.Pearson(c1, c3);
Console.WriteLine("HERE IS THE CORRELATION: " + corr1);
Console.WriteLine("HERE IS THE CORRELATION: " + corr2);
//bool alldone = false, done1 = false, done2 = false, done3 = false;
//int onestarting=0,twostarting=0,threestarting=0;
//while (!alldone)
//{
// if (!done1)
// {
// if (chromXYData1.Xvalues[onestarting]==minx)
// {
// done1 = true;
// }
// else
// {
// }
// }
// if (!done2)
// {
// }
// if (!done3)
// {
// }
// alldone = done1 && done2 && done3;
//}
}
public void Test1()
{
var testFile =
@"D:\Data\Orbitrap\BrianIQTesting\QC_Shew_11_02_pt5-b_6Jun11_Sphinx_11-03-27.RAW";
var peaksTestFile =
@"D:\Data\Orbitrap\BrianIQTesting\QC_Shew_11_02_pt5-b_6Jun11_Sphinx_11-03-27_peaks.txt";
var run = RunUtilities.CreateAndLoadPeaks(testFile, peaksTestFile);
var target = new LcmsFeatureTarget();
target.ID = 0;
target.MZ = 715.39214;
target.ScanLCTarget = 7343;
target.ElutionTimeUnit = Globals.ElutionTimeUnit.ScanNum;
run.CurrentMassTag = target;
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag);
double chromPeakGeneratorTolInPPM = 20;
var chromGeneratorMode = Globals.ChromatogramGeneratorMode.MZ_BASED;
var chromGen = new PeakChromatogramGenerator(chromPeakGeneratorTolInPPM, chromGeneratorMode);
// If we want to use the Execute Command
//BLL .1 and .5 NET windows work. .02 NET window does not BR and SN was set to 1 however)
chromGen.ChromWindowWidthForNonAlignedData = .02F;
var pointsToSmooth = 5;
var chromSmoother = new SavitzkyGolaySmoother(pointsToSmooth, 2);
//BLL We also tried to set the BR and SIG NOISE to 0. This did not work
var chromPeakDetectorPeakBR = 0.5;
var chromPeakDetectorSigNoise = 0.5;
var chromPeakDetector = new ChromPeakDetector(chromPeakDetectorPeakBR, chromPeakDetectorSigNoise);
var chromPeakSelectorParameters = new ChromPeakSelectorParameters();
chromPeakSelectorParameters.PeakSelectorMode = Globals.PeakSelectorMode.ClosestToTarget;
var chromPeakSelector = new BasicChromPeakSelector(chromPeakSelectorParameters);
var smartChromPeakParameters = new SmartChromPeakSelectorParameters();
var smartChromPeakSelector = new SmartChromPeakSelector(smartChromPeakParameters);
//this generates an extracted ion chromatogram
// Since we are not using the built in generator,
chromGen.Execute(run.ResultCollection);
//this smooths the data - very important step!
//BLL. This didnt work for me when we first started, instead of using the NET window above.
//chromGen.GenerateChromatogram(run,
// target.ScanLCTarget - 300,
// target.ScanLCTarget + 300,
// target.MZ,
// chromPeakGeneratorTolInPPM);
chromSmoother.Execute(run.ResultCollection);
//this detects peaks within an extracted ion chromatogram
chromPeakDetector.Execute(run.ResultCollection);
//this selects the peak
chromPeakSelector.Execute(run.ResultCollection);
//smartChromPeakSelector.Execute(run.ResultCollection);
//TestUtilities.DisplayXYValues(run.XYData);
TestUtilities.DisplayPeaks(run.PeakList);
Console.WriteLine("Number of peaks detected = " + run.PeakList.Count);
Console.WriteLine("Selected peak= " + result.ChromPeakSelected);
}
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);
}
}
public void checkO16O18ChromGenMode_test1()
{
//
var testFile = @"D:\Data\O16O18\Weijun\TechTest_O18_02\TechTest_O18_02_RunA_10Dec09_Doc_09-11-08.RAW";
var massTagFile = @"C:\Users\d3x720\Documents\PNNL\My_DataAnalysis\2011\O16O18_TargetedProcessing\Targets\MassTags_MousePlasma_1709_allChargeStates_nonRedundant.txt";
var peakTestFile = testFile.Replace(".RAW", "_peaks.txt");
var run = RunUtilities.CreateAndLoadPeaks(testFile, peakTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 20746149;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();
TargetedWorkflowParameters parameters = new O16O18WorkflowParameters();
parameters.ChromNETTolerance = 0.1;
parameters.MSToleranceInPPM = 10;
parameters.ChromGeneratorMode = DeconTools.Backend.Globals.ChromatogramGeneratorMode.O16O18_THREE_MONOPEAKS;
parameters.ChromPeakDetectorPeakBR = 1;
var workflow = new O16O18Workflow(run, parameters);
workflow.Execute();
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag);
result.DisplayToConsole();
// Assert.AreEqual(3498, result.ScanSet.PrimaryScanNumber);
Console.WriteLine("O16O18 ChromMode PeaksWithinTol = " + result.NumChromPeaksWithinTolerance);
Console.WriteLine("O16O18 ChromMode HQPeaksWithinTol = " + result.NumQualityChromPeaks);
//foreach (var item in workflow.ChromPeaksDetected)
//{
// Console.WriteLine("peak\t" + item.XValue.ToString("0.0") + "\t" + item.Height.ToString("0"));
//}
// TestUtilities.DisplayXYValues(workflow.ChromatogramXYData);
parameters.ChromGeneratorMode = Globals.ChromatogramGeneratorMode.MOST_ABUNDANT_PEAK;
workflow = new O16O18Workflow(run, parameters);
workflow.Execute();
result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag);
Console.WriteLine("MonoChromMode PeaksWithinTol = " + result.NumChromPeaksWithinTolerance);
Console.WriteLine("O16O18 ChromMode HQPeaksWithinTol = " + result.NumQualityChromPeaks);
// TestUtilities.DisplayXYValues(workflow.ChromatogramXYData);
//foreach (var item in workflow.ChromPeaksDetected)
//{
// Console.WriteLine("peak\t" + item.XValue.ToString("0.0") + "\t" + item.Height.ToString("0"));
//}
result.DisplayToConsole();
}