public void checkRetrievalOfScanValueForAGivenNET()
{
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 netAlignmentInfoImporter = new NETAlignmentFromTextImporter(NETAlignmentInfoFilename);
var scanNETdata = netAlignmentInfoImporter.Import();
run.NetAlignmentInfo.SetScanToNETAlignmentData(scanNETdata);
var testNET1 = 0.95f;
var testNET2 = 0.08f;
var scan1 = (int)run.NetAlignmentInfo.GetScanForNet(testNET1);
var scan2 = (int)run.NetAlignmentInfo.GetScanForNet(testNET2);
Assert.AreEqual(18231, scan1);
Assert.AreEqual(1113, scan2);
//foreach (var item in scanNETdata)
//{
// Console.WriteLine(item);
//}
//Console.WriteLine();
//Console.WriteLine();
//Console.WriteLine(scan1 + " was returned for NET= " + testNET1);
}
public void Import_NET_And_MassAlignment_Test1()
{
string mzAlignmentInfoFilename = Path.Combine(FileRefs.OutputFolderPath, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_MZAlignment.txt");
string NETAlignmentInfoFilename = Path.Combine(FileRefs.OutputFolderPath, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_ScanNetAlignment.txt");
RunFactory rf = new RunFactory();
Run run = rf.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
MassAlignmentInfoFromTextImporter importer = new MassAlignmentInfoFromTextImporter(mzAlignmentInfoFilename);
run.AlignmentInfo = importer.Import();
NETAlignmentFromTextImporter netAlignmentInfoImporter = new NETAlignmentFromTextImporter(NETAlignmentInfoFilename);
netAlignmentInfoImporter.ImportIntoAlignmentInfo(run.AlignmentInfo); //this will append the NET alignment info to the AlignmentInfo object
float testScan = 6439;
float testMZ = 698.875137f; //QCSHEW massTag 37003; m/z 698.875137 (2+) See Redmine issue 627: http://redmine.pnl.gov/issues/627
float ppmshift = run.AlignmentInfo.GetPPMShiftFromTimeMZ(testScan, testMZ);
Console.WriteLine("ppm shift = " + ppmshift);
float testScan2 = 6005;
float testNET1 = run.AlignmentInfo.GetNETFromTime(testScan2);
Assert.AreEqual(0.3253423m, (decimal)testNET1);
Assert.AreEqual(-4.3, (decimal)Math.Round(ppmshift, 1));
}
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 ImportNET_and_Try_Alignment_Test1()
{
string importFilename = Path.Combine(FileRefs.OutputFolderPath, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_ScanNetAlignment.txt");
RunFactory rf = new RunFactory();
Run run = rf.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
NETAlignmentFromTextImporter importer = new NETAlignmentFromTextImporter(importFilename);
run.AlignmentInfo = importer.Import();
float testScan = 6005;
float testNET1 = run.AlignmentInfo.GetNETFromTime(testScan);
Assert.AreEqual(0.3253423m, (decimal)testNET1);
}
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 ImportNET_and_Try_Alignment_Test2()
{
var importFilename = 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 NETAlignmentFromTextImporter(importFilename);
importer.Execute(run);
var testScan = 6005;
var testNET1 = run.NetAlignmentInfo.GetNETValueForScan(testScan);
Assert.AreEqual(0.3252918m, (decimal)Math.Round(testNET1, 7));
Assert.IsTrue(run.NETIsAligned);
}
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);
}