public void Import_NET_And_MassAlignment_Test1()
{
var mzAlignmentInfoFilename = Path.Combine(FileRefs.ImportedData, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_MZAlignment.txt");
var NETAlignmentInfoFilename = Path.Combine(FileRefs.ImportedData, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_ScanNetAlignment.txt");
var rf = new RunFactory();
var run = rf.CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var importer = new MassAlignmentInfoFromTextImporter(mzAlignmentInfoFilename);
var massAlignmentData = importer.Import();
var massAlignmentInfo = new MassAlignmentInfoLcmsWarp();
massAlignmentInfo.SetMassAlignmentData(massAlignmentData);
run.MassAlignmentInfo = massAlignmentInfo;
var netAlignmentInfoImporter = new NETAlignmentFromTextImporter(NETAlignmentInfoFilename);
var scanNETdata = netAlignmentInfoImporter.Import();
run.NetAlignmentInfo.SetScanToNETAlignmentData(scanNETdata);
float testScan = 6439;
var testMZ = 698.875137f; //QCSHEW massTag 37003; m/z 698.875137 (2+) See Redmine issue 627: http://redmine.pnl.gov/issues/627
var ppmshift = run.MassAlignmentInfo.GetPpmShift(testMZ, (int)testScan);
Console.WriteLine("ppm shift = " + ppmshift);
var testScan2 = 6005;
var testNET1 = run.NetAlignmentInfo.GetNETValueForScan(testScan2);
Assert.AreEqual(0.3252918m, (decimal)Math.Round(testNET1, 7));
Assert.AreEqual(-4.3, (decimal)Math.Round(ppmshift, 1));
}
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 ImportMassAndTimePPMCorrections_and_Try_Alignment_Test1()
{
var importFilename = Path.Combine(FileRefs.ImportedData, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_MZAlignment.txt");
var rf = new RunFactory();
var run = rf.CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var importer = new MassAlignmentInfoFromTextImporter(importFilename);
var massAlignmentData = importer.Import();
var massAlignmentInfo = new MassAlignmentInfoLcmsWarp();
massAlignmentInfo.SetMassAlignmentData(massAlignmentData);
run.MassAlignmentInfo = massAlignmentInfo;
float testScan = 6439;
var testMZ = 698.875137f; //QCSHEW massTag 37003; m/z 698.875137 (2+) See Redmine issue 627: http://redmine.pnl.gov/issues/627
var ppmshift = run.MassAlignmentInfo.GetPpmShift(testMZ, (int)testScan);
Console.WriteLine("ppm shift = " + ppmshift);
Assert.AreEqual(-4.3, (decimal)Math.Round(ppmshift, 1));
}
public void Execute(Run run)
{
Check.Require(run != null, "Run is not defined.");
Check.Require(_featuresToBeAligned.HasResults, "Features for alignment have not been defined.");
Check.Require(_massTagList != null && _massTagList.Count > 0, "The reference set of MassTags used in alignment have not been defined.");
var lcmswarpAlignmentInfo = GetAlignment(_massTagList, _featuresToBeAligned.Results);
var massAlignmentInfo = new MassAlignmentInfoLcmsWarp();
massAlignmentInfo.AlignmentInfo = lcmswarpAlignmentInfo;
run.MassAlignmentInfo = massAlignmentInfo;
}
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 check_alignment_of_MZ()
{
var mzAlignmentInfoFilename = Path.Combine(FileRefs.ImportedData, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_MZAlignment.txt");
var NETAlignmentInfoFilename = Path.Combine(FileRefs.ImportedData, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_ScanNetAlignment.txt");
var rf = new RunFactory();
var run = rf.CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var importer = new MassAlignmentInfoFromTextImporter(mzAlignmentInfoFilename);
var massAlignmentData = importer.Import();
var massAlignmentInfo = new MassAlignmentInfoLcmsWarp();
massAlignmentInfo.SetMassAlignmentData(massAlignmentData);
run.MassAlignmentInfo = massAlignmentInfo;
var netAlignmentInfoImporter = new NETAlignmentFromTextImporter(NETAlignmentInfoFilename);
var scanNETdata = netAlignmentInfoImporter.Import();
run.NetAlignmentInfo.SetScanToNETAlignmentData(scanNETdata);
float testScan = 6439;
var theorMZ = 698.875137f; //QCSHEW massTag 37003; m/z 698.875137 (2+) See Redmine issue 627: http://redmine.pnl.gov/issues/627
var ppmshift = run.MassAlignmentInfo.GetPpmShift(theorMZ, (int)testScan);
Console.WriteLine("ppm shift = " + ppmshift);
var observedMZ = 698.8721;
var alignedTargetMZ = run.GetTargetMZAligned(theorMZ);
var differenceInMZ = Math.Abs(observedMZ - alignedTargetMZ);
Console.WriteLine("theor m/z of monoisotopic peak = " + theorMZ.ToString("0.0000"));
Console.WriteLine("observed m/z of monoisotopic peak = " + observedMZ.ToString("0.0000"));
Console.WriteLine("aligned theor m/z = " + alignedTargetMZ.ToString("0.00000"));
Assert.IsTrue(differenceInMZ < 0.001);
}
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 static bool AlignRunUsingAlignmentInfoInFiles(Run run, string alignmentDataFolder = "")
{
bool alignmentSuccessful;
string basePath;
if (string.IsNullOrEmpty(alignmentDataFolder))
{
basePath = run.DataSetPath;
}
else
{
if (Directory.Exists(alignmentDataFolder))
{
basePath = alignmentDataFolder;
}
else
{
throw new DirectoryNotFoundException(
"Cannot align dataset. Source alignment folder does not exist. Alignment folder = " +
alignmentDataFolder);
}
}
var expectedMZAlignmentFile = Path.Combine(basePath, run.DatasetName + "_MZAlignment.txt");
var expectedNETAlignmentFile = Path.Combine(basePath, run.DatasetName + "_NETAlignment.txt");
//first will try to load the multiAlign alignment info
if (File.Exists(expectedMZAlignmentFile))
{
var importer = new MassAlignmentInfoFromTextImporter(expectedMZAlignmentFile);
var massAlignmentData = importer.Import();
var massAlignmentInfo = new MassAlignmentInfoLcmsWarp();
massAlignmentInfo.SetMassAlignmentData(massAlignmentData);
run.MassAlignmentInfo = massAlignmentInfo;
}
if (File.Exists(expectedNETAlignmentFile))
{
var netAlignmentInfoImporter = new NETAlignmentFromTextImporter(expectedNETAlignmentFile);
var scanNETList = netAlignmentInfoImporter.Import();
NetAlignmentInfo netAlignmentInfo = new NetAlignmentInfoBasic(run.MinLCScan, run.MaxLCScan);
netAlignmentInfo.SetScanToNETAlignmentData(scanNETList);
run.NetAlignmentInfo = netAlignmentInfo;
}
//if still not aligned, try to get the NET alignment from UMCs file. (this is the older way to do it)
if (run.NETIsAligned)
{
alignmentSuccessful = true;
}
else
{
var alignmentDirInfo = new DirectoryInfo(basePath);
var umcFileInfo = alignmentDirInfo.GetFiles("*_umcs.txt");
var umcFileCount = umcFileInfo.Count();
if (umcFileCount == 1)
{
var targetUmcFileName = umcFileInfo.First().FullName;
var importer = new UMCFileImporter(targetUmcFileName, '\t');
var umcs = importer.Import();
var scannetPairs = umcs.GetScanNETLookupTable();
NetAlignmentInfo netAlignmentInfo = new NetAlignmentInfoBasic(run.MinLCScan, run.MaxLCScan);
netAlignmentInfo.SetScanToNETAlignmentData(scannetPairs);
run.NetAlignmentInfo = netAlignmentInfo;
Console.WriteLine(run.DatasetName + " aligned.");
alignmentSuccessful = true;
}
else if (umcFileCount > 1)
{
var expectedUMCName = Path.Combine(basePath, run.DatasetName + "_UMCs.txt");
if (File.Exists(expectedUMCName))
{
var importer = new UMCFileImporter(expectedUMCName, '\t');
var umcs = importer.Import();
var scannetPairs = umcs.GetScanNETLookupTable();
NetAlignmentInfo netAlignmentInfo = new NetAlignmentInfoBasic(run.MinLCScan, run.MaxLCScan);
netAlignmentInfo.SetScanToNETAlignmentData(scannetPairs);
run.NetAlignmentInfo = netAlignmentInfo;
Console.WriteLine(run.DatasetName + " NET aligned using UMC file: " + expectedUMCName);
alignmentSuccessful = true;
}
else
{
throw new FileNotFoundException("Trying to align dataset: " + run.DatasetName +
" but UMC file not found.");
}
}
else
{
Console.WriteLine(run.DatasetName + " is NOT NET aligned.");
alignmentSuccessful = false;
}
}
//mass is still not aligned... use data in viper output file: _MassAndGANETErrors_BeforeRefinement.txt
if (run.MassIsAligned == false)
{
var expectedViperMassAlignmentFile = Path.Combine(basePath, run.DatasetName + "_MassAndGANETErrors_BeforeRefinement.txt");
if (File.Exists(expectedViperMassAlignmentFile))
{
var importer = new ViperMassCalibrationLoader(expectedViperMassAlignmentFile);
var viperCalibrationData = importer.ImportMassCalibrationData();
var massAlignmentInfo = new MassAlignmentInfoLcmsWarp();
massAlignmentInfo.SetMassAlignmentData(viperCalibrationData);
run.MassAlignmentInfo = massAlignmentInfo;
Console.WriteLine(run.DatasetName + "- mass aligned using file: " + expectedViperMassAlignmentFile);
alignmentSuccessful = true;
}
else
{
Console.WriteLine(run.DatasetName + " is NOT mass aligned");
}
}
return(alignmentSuccessful);
}
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);
}