public void ApplyViperMassAlignmentDataFromViperTest1()
{
var testFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
var run = new RunFactory().CreateRun(testFile);
var calibrationData = new ViperMassCalibrationData();
calibrationData.MassError = -3.6;
var massAlignmentInfo = new MassAlignmentInfoLcmsWarp();
massAlignmentInfo.SetMassAlignmentData(calibrationData);
run.MassAlignmentInfo = massAlignmentInfo;
var testMZ = 974.504343924692;
var alignedMZ = run.GetAlignedMZ(testMZ);
var ppmDiff = (testMZ - alignedMZ) / testMZ * 1e6;
Console.WriteLine("input m/z= " + testMZ);
Console.WriteLine("aligned m/z= " + alignedMZ);
Console.WriteLine("ppmDiff= " + ppmDiff);
Assert.AreEqual(-3.6, (decimal)Math.Round(ppmDiff, 1));
}
public void ensureAlignment_was_executed()
{
var run = new RunFactory().CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var alignmentFeaturesFile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\AlignmentInfo\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_READONLY_alignedFeatures.txt";
var importer = new UnlabelledTargetedResultFromTextImporter(alignmentFeaturesFile);
var repo = importer.Import();
var massTagFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Targets\QCShew_Formic_MassTags_Bin10_all.txt";
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var parameters = new NETAndMassAlignerParameters();
var aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.TargetList);
var scan = 7835;
var theorMZ = 780.08485; //massTagID = 24701 (+3)
var obsMZ = 780.0824;
var netBeforeAlignment = run.NetAlignmentInfo.GetNETValueForScan(scan);
var mzBeforeAlignment = run.GetAlignedMZ(obsMZ);
aligner.Execute(run);
var netAfterAlignment = run.NetAlignmentInfo.GetNETValueForScan(scan);
var mzAfterAlignment = run.GetAlignedMZ(obsMZ);
Console.WriteLine("NET before alignment = " + netBeforeAlignment);
Console.WriteLine("NET after alignment = " + netAfterAlignment);
Console.WriteLine("Theor MZ = " + theorMZ);
Console.WriteLine("MZ before alignment = " + mzBeforeAlignment);
Console.WriteLine("MZ after alignment = " + mzAfterAlignment);
Console.WriteLine("PPMDiff before alignment = " + (theorMZ - mzBeforeAlignment) / theorMZ * 1e6);
Console.WriteLine("PPMDiff after alignment = " + (theorMZ - mzAfterAlignment) / theorMZ * 1e6);
}
public void LoadAndApplyMassAlignmentFromViperDataTest1()
{
var testFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
var run = new RunFactory().CreateRun(testFile);
var viperMassAlignmentFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\AlignmentInfo\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_MassAndGANETErrors_BeforeRefinement.txt";
var loader = new ViperMassCalibrationLoader(viperMassAlignmentFile);
/*
* From unit test: targetedWorkflow_alignUsingDataFromFiles
* TargetID = 24702
* ChargeState = 3
* theor monomass= 2920.5319802
* theor m/z= 974.517936556667
* obs monomass= 2920.49120230408
* obs m/z= 974.504343924692
* ppmError before= 13.9597398284934
* ppmError after= 10.8899784905986
* calibrated mass= 2920.50017566955
* calibrated mass2= 2920.50017566955
* Database NET= 0.4197696
* Result NET= 0.42916464805603
* Result NET Error= -0.00934833288192749
* NumChromPeaksWithinTol= 3
*
*
*/
var calibrationData = loader.ImportMassCalibrationData();
var massAlignmentInfo = new MassAlignmentInfoLcmsWarp();
massAlignmentInfo.SetMassAlignmentData(calibrationData);
run.MassAlignmentInfo = massAlignmentInfo;
var testMZ = 974.504343924692;
var alignedMZ = run.GetAlignedMZ(testMZ);
var ppmDiff = (testMZ - alignedMZ) / testMZ * 1e6;
Console.WriteLine("input m/z= " + testMZ);
Console.WriteLine("aligned m/z= " + alignedMZ);
Console.WriteLine("ppmDiff= " + ppmDiff);
Assert.AreEqual(-3.6, (decimal)Math.Round(ppmDiff, 1));
}
public void GetCalibratedMass1()
{
//see https://jira.pnnl.gov/jira/browse/OMCS-870
var testFile =
@"\\protoapps\DataPkgs\Public\2013\743_Mycobacterium_tuberculosis_Cys_and_Ser_ABP\IQ_Analysis\Testing\LNA_A_Stat_Sample_SC_28_LNA_ExpA_Expo_Stat_SeattleBioMed_15Feb13_Cougar_12-12-36.raw";
var run = new RunFactory().CreateRun(testFile);
var calibrationData = new ViperMassCalibrationData();
calibrationData.MassError = 4.8;
var massAlignmentInfo = new MassAlignmentInfoLcmsWarp();
massAlignmentInfo.SetMassAlignmentData(calibrationData);
run.MassAlignmentInfo = massAlignmentInfo;
var observedMZ = 440.5887078;
var theorMZ = 440.5858315;
var calibratedMZ = run.GetAlignedMZ(observedMZ);
Assert.AreEqual(440.5866m, (decimal)Math.Round(calibratedMZ, 4));
var ppmDiffBefore = (observedMZ - theorMZ) / theorMZ * 1e6;
var ppmDiffAfter = (calibratedMZ - theorMZ) / theorMZ * 1e6;
Console.WriteLine("input m/z= " + observedMZ);
Console.WriteLine("calibrated m/z= " + calibratedMZ);
Console.WriteLine("ppmDiffBeforeCalibration= " + ppmDiffBefore);
Console.WriteLine("ppmDiffAftereCalibration= " + ppmDiffAfter);
var theorMZToLookForInRawData = run.GetTargetMZAligned(theorMZ);
var ppmDiffTheor = (theorMZToLookForInRawData - theorMZ) / theorMZ * 1e6;
Console.WriteLine();
Console.WriteLine("Theor m/z = " + theorMZ);
Console.WriteLine("Theor m/z to look for = " + theorMZToLookForInRawData);
Console.WriteLine("ppmDiff = " + ppmDiffTheor);
Assert.AreEqual(4.8m, (decimal)Math.Round(ppmDiffTheor, 1));
}
public void AlignmentParameterTesting2()
{
var run = new RunFactory().CreateRun(@"D:\Data\Orbitrap\Subissue01\QC_Shew_10_01-pt5-1_8Feb10_Doc_09-12-24.RAW");
var alignmentFeaturesFile = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\AlignmentInfo\QC_Shew_10_01-pt5-1_8Feb10_Doc_09-12-24_alignedFeatures.txt";
var importer = new UnlabelledTargetedResultFromTextImporter(alignmentFeaturesFile);
var repo = importer.Import();
var massTagFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Targets\QCShew_Formic_MassTags_Bin10_all.txt";
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var parameters = new NETAndMassAlignerParameters();
var aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.TargetList);
var sb = new StringBuilder();
sb.Append("mtid\tscanLC\ttheorMZ\tobsMZ\talignedMZ\tppmErrorBefore\tppmErrorAfter\n");
parameters.MassCalibrationWindow = 20;
parameters.MassCalibrationNumMassDeltaBins = 100;
// int[] massCalXSliceValues = { 3, 6, 9, 12, 15 };
int[] massCalXSliceValues = { 15 };
foreach (var xsliceVal in massCalXSliceValues)
{
var ppmErrorsBefore = new List<double>();
var ppmErrorsAfter = new List<double>();
parameters.MassCalibrationNumXSlices = (short)xsliceVal;
aligner.AlignerParameters = parameters;
aligner.Execute(run);
foreach (var result in repo.Results)
{
var mt = mtc.TargetList.Where(p => p.ID == result.TargetID).Where(p => p.ChargeState == result.ChargeState).First();
var theorMZ = mt.MZ;
var obsMZ = result.MonoMZ;
double scan = result.ScanLC;
var alignedMZ = run.GetAlignedMZ(obsMZ, scan);
var ppmErrorBefore = (theorMZ - obsMZ) / theorMZ * 1e6;
var ppmErrorAfter = (theorMZ - alignedMZ) / theorMZ * 1e6;
sb.Append(result.TargetID + "\t" + result.ScanLC + "\t" + theorMZ.ToString("0.00000") + "\t" + obsMZ.ToString("0.00000") + "\t" + alignedMZ.ToString("0.00000") + "\t" + ppmErrorBefore.ToString("0.0") + "\t" + ppmErrorAfter.ToString("0.0"));
sb.Append(Environment.NewLine);
ppmErrorsAfter.Add(ppmErrorAfter);
ppmErrorsBefore.Add(ppmErrorBefore);
}
Console.WriteLine(sb.ToString());
Console.WriteLine();
Console.WriteLine();
Console.WriteLine("Average ppm error before alignment = " + ppmErrorsBefore.Average().ToString("0.00"));
Console.WriteLine("Average ppm error after alignment = " + ppmErrorsAfter.Average().ToString("0.00"));
Console.WriteLine();
Console.WriteLine();
Console.WriteLine(xsliceVal + "\t" + ppmErrorsBefore.Average().ToString("0.00") + "\t" + ppmErrorsAfter.Average().ToString("0.00"));
}
}
public void Issue0725_AlignmentProblemsTest1()
{
var run = new RunFactory().CreateRun(@"D:\Data\Orbitrap\Issue0725_badAlignment\QC_Shew_10_03-2_100min_06May10_Tiger_10-04-08.RAW");
var alignmentFeaturesFile = run.Filename.Replace(".RAW", "_alignedFeatures.txt");
var importer = new UnlabelledTargetedResultFromTextImporter(alignmentFeaturesFile);
var repo = importer.Import();
var massTagFile = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\MassTags\QCShew_Formic_MassTags_for_alignment.txt";
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var parameters = new NETAndMassAlignerParameters();
var aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.TargetList);
var sb = new StringBuilder();
sb.Append("mtid\tscanLC\ttheorMZ\tobsMZ\talignedMZ\tppmErrorBefore\tppmErrorAfter\n");
parameters.MassCalibrationWindow = 50;
parameters.MassCalibrationNumMassDeltaBins = 100;
int[] massCalXSliceValues = { 3, 6, 9, 10, 12, 15,18,20 };
//int[] massCalXSliceValues = { 6 };
foreach (var xsliceVal in massCalXSliceValues)
{
var ppmErrorsBefore = new List<double>();
var ppmErrorsAfter = new List<double>();
parameters.MassCalibrationNumXSlices = (short)xsliceVal;
aligner.AlignerParameters = parameters;
aligner.Execute(run);
foreach (var result in repo.Results)
{
var mt = mtc.TargetList.Where(p => p.ID == result.TargetID).Where(p => p.ChargeState == result.ChargeState).First();
var theorMZ = mt.MZ;
var obsMZ = result.MonoMZ;
double scan = result.ScanLC;
var alignedMZ = run.GetAlignedMZ(obsMZ, scan);
var ppmErrorBefore = (theorMZ - obsMZ) / theorMZ * 1e6;
var ppmErrorAfter = (theorMZ - alignedMZ) / theorMZ * 1e6;
double theorNET = mt.NormalizedElutionTime;
double obsNET = result.NET;
var alignedNET = run.NetAlignmentInfo.GetNETValueForScan((int) scan);
sb.Append(result.TargetID + "\t" + result.ScanLC + "\t" + theorMZ.ToString("0.00000") + "\t" + obsMZ.ToString("0.00000") + "\t" + alignedMZ.ToString("0.00000") + "\t" + ppmErrorBefore.ToString("0.0") + "\t" + ppmErrorAfter.ToString("0.0") + "\t" + theorNET.ToString("0.0000") + "\t" + obsNET.ToString("0.0000") + "\t" + alignedNET.ToString("0.0000"));
//sb.Append(result.MassTagID + "\t" + result.ScanLC + "\t" + theo
sb.Append(Environment.NewLine);
ppmErrorsAfter.Add(ppmErrorAfter);
ppmErrorsBefore.Add(ppmErrorBefore);
}
// Console.WriteLine(sb.ToString());
//Console.WriteLine();
//Console.WriteLine();
//Console.WriteLine("Average ppm error before alignment = " + filterWithGrubbsApplied(ppmErrorsBefore).Average().ToString("0.00"));
//Console.WriteLine("Average ppm error after alignment = " + filterWithGrubbsApplied(ppmErrorsAfter).Average().ToString("0.00"));
//Console.WriteLine();
//Console.WriteLine();
Console.WriteLine(xsliceVal + "\t" + filterWithGrubbsApplied(ppmErrorsBefore).Average().ToString("0.00") + "\t" + filterWithGrubbsApplied(ppmErrorsAfter).Average().ToString("0.00"));
}
}
public void AlignmentParameterTesting1()
{
var run = new RunFactory().CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var alignmentFeaturesFile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_READONLY_alignedFeatures.txt";
var importer = new UnlabelledTargetedResultFromTextImporter(alignmentFeaturesFile);
var repo = importer.Import();
var massTagFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Targets\QCShew_Formic_MassTags_Bin10_all.txt";
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var parameters = new NETAndMassAlignerParameters();
var aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.TargetList);
var sb = new StringBuilder();
sb.Append("theorMZ\tobsMZ\talignedMZ\tppmErrorBefore\tppmErrorAfter\n");
parameters.MassCalibrationWindow = 50;
parameters.MassCalibrationNumMassDeltaBins = 100;
int[]massCalXSliceValues = {3,6,9,12,15,20,30,50};
foreach (var xsliceVal in massCalXSliceValues)
{
var ppmErrorsBefore = new List<double>();
var ppmErrorsAfter = new List<double>();
parameters.MassCalibrationNumXSlices =(short)xsliceVal;
aligner.AlignerParameters = parameters;
aligner.Execute(run);
foreach (var result in repo.Results)
{
var mt = mtc.TargetList.Where(p => p.ID == result.TargetID).Where(p => p.ChargeState == result.ChargeState).First();
var theorMZ = mt.MZ;
var obsMZ = result.MonoMZ;
double scan = result.ScanLC;
var alignedMZ = run.GetAlignedMZ(obsMZ, scan);
var ppmErrorBefore = (theorMZ - obsMZ) / theorMZ * 1e6;
var ppmErrorAfter = (theorMZ - alignedMZ) / theorMZ * 1e6;
sb.Append(result.TargetID + "\t" + result.ScanLC + "\t" + theorMZ.ToString("0.00000") + "\t" + obsMZ.ToString("0.00000") + "\t" + alignedMZ.ToString("0.00000") + "\t" + ppmErrorBefore.ToString("0.0") + "\t" + ppmErrorAfter.ToString("0.0"));
sb.Append(Environment.NewLine);
ppmErrorsAfter.Add(ppmErrorAfter);
ppmErrorsBefore.Add(ppmErrorBefore);
}
Console.WriteLine(xsliceVal + "\t" + ppmErrorsBefore.Average().ToString("0.00") + "\t"+ ppmErrorsAfter.Average().ToString("0.00"));
//Console.WriteLine(sb.ToString());
//Console.WriteLine();
//Console.WriteLine();
//Console.WriteLine("Average ppm error before alignment = " + ppmErrorsBefore.Average().ToString("0.00"));
//Console.WriteLine("Average ppm error after alignment = " + ppmErrorsAfter.Average().ToString("0.00"));
}
}
