public RapidDeconvolutor(double minPeptideToBackgroundRatio, DeconResultComboMode comboMode)
{
this.minPeptideToBackgroundRatio = minPeptideToBackgroundRatio;
this.resultCombiningMode = comboMode;
this.IsNewFitCalculationPerformed = true;
this.fitScoreCalculator = new DeconTools.Backend.ProcessingTasks.FitScoreCalculators.DeconToolsFitScoreCalculator();
this.targetedFeatureFinder = new BasicTFF();
}
public void Test1()
{
double featureFinderTol = 15;
var featureFinderRequiresMonoPeak = false;
var n14n15Util = new N14N15TestingUtilities();
//get MS
var massSpectrum = n14n15Util.GetSpectrumAMTTag23140708_Z3_Sum3(); //this is the diff b/w previous test and this one
var mt23140708 = n14n15Util.CreateMT23140708_Z3();
var featureGen2 = new JoshTheorFeatureGenerator();
featureGen2.GenerateTheorFeature(mt23140708);
//get ms peaks
var peakDet = new DeconToolsPeakDetectorV2(1.3, 2, Globals.PeakFitType.QUADRATIC, false);
var msPeakList = peakDet.FindPeaks(massSpectrum, 0, 0);
var bff = new BasicTFF(featureFinderTol, featureFinderRequiresMonoPeak);
var n14Profile = bff.FindMSFeature(msPeakList, mt23140708.IsotopicProfile);
var theorXYData = mt23140708.IsotopicProfile.GetTheoreticalIsotopicProfileXYData(n14Profile.GetFWHM());
var theorMaxY = theorXYData.Yvalues.Max();
double obsMaxY = n14Profile.getMostIntensePeak().Height;
for (var i = 0; i < theorXYData.Xvalues.Length; i++)
{
theorXYData.Yvalues[i] = theorXYData.Yvalues[i] * obsMaxY;
}
offsetDistribution(theorXYData, mt23140708.IsotopicProfile, n14Profile);
var subtracted = XYDataUtilities.SubtractXYData(massSpectrum, theorXYData, n14Profile.MonoPeakMZ - 1,
n14Profile.MonoPeakMZ + 3, 0.01);
var outputFileMS = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\TextFile\massSpectrum1.txt";
var outputFileMSSubtracted = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\TextFile\massSpectrum1_withDataSubtracted.txt";
TestUtilities.WriteToFile(massSpectrum, outputFileMS);
TestUtilities.WriteToFile(subtracted, outputFileMSSubtracted);
// XYDataUtilities.NormalizeXYData()
}
public void test1()
{
Run run = new XCaliburRun(xcaliburTestfile);
List <MassTag> mass_tagList = TestUtilities.CreateTestMassTagList();
MassTag mt = mass_tagList[0];
run.CurrentScanSet = new ScanSet(9017, new int[] { 9010, 9017, 9024 });
run.CurrentMassTag = mt;
MSGeneratorFactory msgenFactory = new MSGeneratorFactory();
Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType);
DeconToolsV2.Peaks.clsPeakProcessorParameters peakParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(2, 1.3, true, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC);
Task mspeakDet = new DeconToolsPeakDetector(peakParams);
Task theorFeatureGen = new TomTheorFeatureGenerator();
Task targetedFeatureFinder = new BasicTFF(0.01);
IsotopicProfileFitScoreCalculator fitScoreCalc = new IsotopicProfileFitScoreCalculator();
msgen.Execute(run.ResultCollection);
//run.XYData.Display();
mspeakDet.Execute(run.ResultCollection);
theorFeatureGen.Execute(run.ResultCollection);
targetedFeatureFinder.Execute(run.ResultCollection);
fitScoreCalc.Execute(run.ResultCollection);
MassTagResultBase result = run.ResultCollection.GetMassTagResult(mt);
TestUtilities.DisplayIsotopicProfileData(result.IsotopicProfile);
Console.WriteLine("Fit val = " + result.IsotopicProfile.Score);
/*
*
*
* ------------------- MassTag = 24769---------------------------
* monoMass = 2086.0595; monoMZ = 1044.0370; ChargeState = 2; NET = 0.452; Sequence = DFNEALVHQVVVAYAANAR
*
****** Match ******
******NET = 0.452
******ChromPeak ScanNum = 9016.48992535631
******ChromPeak NETVal = 0.453
******ScanSet = { 9010, 9017, 9024, }
******Observed MZ and intensity = 1044.03290771556 1.269842E+07
******------------------------------ end --------------------------
*
*
*
*
*
*/
}
public void n14N15LabelledData_TFFTest1()
{
double featureFinderTol = 15;
var featureFinderRequiresMonoPeak = false;
var n14n15Util = new N14N15TestingUtilities();
//get sample MS from Test Data
var massSpectrum = n14n15Util.GetSpectrumAMTTag23140708_Z3_Sum3(); //this is the diff b/w previous test and this one
var mt23140708 = n14n15Util.CreateMT23140708_Z3();
//get ms peaks
var peakDet = new DeconToolsPeakDetectorV2(1.3, 2, Globals.PeakFitType.QUADRATIC, false);
var msPeakList = peakDet.FindPeaks(massSpectrum, 0, 0);
//TestUtilities.DisplayPeaks(msPeakList);
//generate theor unlabelled profile
var unlabelledfeatureGen = new TomTheorFeatureGenerator();
unlabelledfeatureGen.GenerateTheorFeature(mt23140708);
//generate theor N15-labelled profile
var n15featureGen = new TomTheorFeatureGenerator(Globals.LabellingType.N15, 0.005);
n15featureGen.GenerateTheorFeature(mt23140708);
//find features in experimental data, using the theoretical profiles
var msfeatureFinder = new BasicTFF();
msfeatureFinder.ToleranceInPPM = featureFinderTol;
msfeatureFinder.NeedMonoIsotopicPeak = featureFinderRequiresMonoPeak;
var n14profile = msfeatureFinder.FindMSFeature(msPeakList, mt23140708.IsotopicProfile);
var n15profile = msfeatureFinder.FindMSFeature(msPeakList, mt23140708.IsotopicProfileLabelled);
Console.WriteLine(mt23140708.GetEmpiricalFormulaFromTargetCode());
TestUtilities.DisplayIsotopicProfileData(mt23140708.IsotopicProfile);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(mt23140708.IsotopicProfileLabelled);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(n14profile);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(n15profile);
}
private void GetIsotopicProfilePeaks(List <Peak> peakList, int chargeState, double monoMass, ref IsotopicProfile inputProfile)
{
double toleranceInPPM = 20;
var tff = new BasicTFF(toleranceInPPM);
var theorProfile = new IsotopicProfile();
theorProfile.MonoIsotopicMass = monoMass;
theorProfile.ChargeState = chargeState;
theorProfile.MonoPeakMZ = monoMass / chargeState + Globals.PROTON_MASS;
//a hack to guess how many peaks to include in the theor isotopic profile
int numPeaksToIncludeInProfile = (int)Math.Round(Math.Max(3, 3 + (monoMass - 1000) / 1000));
double monoPeakMZ = monoMass / chargeState + Globals.PROTON_MASS;
for (int i = 0; i < numPeaksToIncludeInProfile; i++)
{
var peak = new MSPeak();
peak.XValue = monoPeakMZ + i * Globals.MASS_DIFF_BETWEEN_ISOTOPICPEAKS / chargeState;
if (i == 0)
{
peak.Height = 1;
}
else
{
peak.Height = 0;
}
theorProfile.Peaklist.Add(peak);
}
var foundIso = tff.FindMSFeature(peakList, theorProfile);
if (foundIso == null)
{
var monoPeak = PeakUtilities.GetPeaksWithinTolerance(peakList, monoPeakMZ, toleranceInPPM).OrderByDescending(p => p.Height).FirstOrDefault();
if (monoPeak != null)
{
inputProfile.Peaklist.Add((MSPeak)monoPeak);
}
}
else
{
inputProfile.Peaklist = new List <MSPeak>(foundIso.Peaklist);
}
}
public void test1()
{
Run run = new XCaliburRun(xcaliburTestfile);
List <MassTag> mass_tagList = TestUtilities.CreateTestMassTagList();
MassTag mt = mass_tagList[0];
run.CurrentScanSet = new ScanSet(9017, new int[] { 9010, 9017, 9024 });
run.CurrentMassTag = mt;
MSGeneratorFactory msgenFactory = new MSGeneratorFactory();
Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType);
DeconToolsV2.Peaks.clsPeakProcessorParameters peakParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(2, 1.3, true, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC);
Task mspeakDet = new DeconToolsPeakDetector(peakParams);
Task theorFeatureGen = new TomTheorFeatureGenerator();
Task targetedFeatureFinder = new BasicTFF(0.01);
IsotopicProfileFitScoreCalculator fitScoreCalc = new IsotopicProfileFitScoreCalculator();
Task exporter = new BasicMTResultSQLiteExporter(exporterOutputFile1);
msgen.Execute(run.ResultCollection);
//run.XYData.Display();
mspeakDet.Execute(run.ResultCollection);
theorFeatureGen.Execute(run.ResultCollection);
targetedFeatureFinder.Execute(run.ResultCollection);
fitScoreCalc.Execute(run.ResultCollection);
exporter.Execute(run.ResultCollection);
exporter.Cleanup();
MassTagResultBase result = run.ResultCollection.GetMassTagResult(mt);
TestUtilities.DisplayIsotopicProfileData(result.IsotopicProfile);
}
public void find_targetMassTag_131959Test1()
{
var run = new RunFactory().CreateRun(xcaliburTestfile);
var masstagImporter = new MassTagFromTextFileImporter(massTagTestList1);
var massTagColl = masstagImporter.Import();
Assert.AreEqual(2719, massTagColl.TargetList.Count);
var chromAligner = new ChromAlignerUsingVIPERInfo();
chromAligner.Execute(run);
var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(xcaliburAllPeaksFile);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
//int mtID = 635428;
var mtID = 131959;
Task peakChromGen = new PeakChromatogramGenerator(20);
Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.SavitzkyGolaySmoother(23, 2);
Task zeroFill = new DeconTools.Backend.ProcessingTasks.ZeroFillers.DeconToolsZeroFiller(3);
Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector(0.5, 1);
Task msPeakDet = new DeconToolsPeakDetectorV2(1.3, 2, Globals.PeakFitType.QUADRATIC, true);
var basicChromPeakSelParam = new ChromPeakSelectorParameters();
basicChromPeakSelParam.NETTolerance = 0.1f;
basicChromPeakSelParam.PeakSelectorMode = Globals.PeakSelectorMode.ClosestToTarget;
Task chromPeakSel = new BasicChromPeakSelector(basicChromPeakSelParam);
Task msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
run.CurrentMassTag = massTagColl.TargetList.Find(p => p.ID == mtID);
var mt = run.CurrentMassTag;
mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS;
Task theorFeatureGen = new TomTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
Task targetedFeatureFinder = new BasicTFF();
Task fitScoreCalc = new IsotopicProfileFitScoreCalculator();
theorFeatureGen.Execute(run.ResultCollection);
Console.WriteLine();
Console.WriteLine();
Console.WriteLine("------------------- MassTag = " + mt.ID + "---------------------------");
Console.WriteLine("monoMass = " + mt.MonoIsotopicMass.ToString("0.0000") + "; monoMZ = " + mt.MZ.ToString("0.0000") + "; ChargeState = " + mt.ChargeState + "; NET = " + mt.NormalizedElutionTime.ToString("0.000") + "; Sequence = " + mt.Code + "; EmpiricalFormula= " + mt.EmpiricalFormula + "\n");
peakChromGen.Execute(run.ResultCollection);
smoother.Execute(run.ResultCollection);
//TestUtilities.DisplayXYValues(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
TestUtilities.DisplayPeaks(run.PeakList);
chromPeakSel.Execute(run.ResultCollection);
msgen.Execute(run.ResultCollection);
//TestUtilities.DisplayXYValues(run.ResultCollection);
msPeakDet.Execute(run.ResultCollection);
targetedFeatureFinder.Execute(run.ResultCollection);
fitScoreCalc.Execute(run.ResultCollection);
var massTagResult = run.ResultCollection.MassTagResultList[mt];
massTagResult.DisplayToConsole();
//Console.WriteLine("------------------------------ end --------------------------");
}
public void test1()
{
Run run = new XCaliburRun(xcaliburTestfile);
MassTagCollection massTagColl = new MassTagCollection();
MassTagIDGenericImporter mtidImporter = new MassTagIDGenericImporter(cysteineMassTagSourceFile1, '\t');
mtidImporter.Import(massTagColl);
MassTagFromSqlDBImporter importer = new MassTagFromSqlDBImporter("MT_Shewanella_ProdTest_P352", "porky");
importer.Import(massTagColl);
Assert.AreEqual(737, massTagColl.MassTagIDList.Count);
Assert.AreEqual(826, massTagColl.MassTagList.Count);
ChromAlignerUsingVIPERInfo chromAligner = new ChromAlignerUsingVIPERInfo();
chromAligner.Execute(run);
PeakImporterFromText peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(xcaliburAllPeaksFile);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
Task peakChromGen = new PeakChromatogramGenerator(20);
Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.DeconToolsSavitzkyGolaySmoother(11, 11, 2);
Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector(0.5, 0.5);
Task chromPeakSel = new DeconTools.Backend.ProcessingTasks.ChromPeakSelector(1, 0.01, Globals.PeakSelectorMode.CLOSEST_TO_TARGET);
MSGeneratorFactory msgenFactory = new MSGeneratorFactory();
Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType);
DeconToolsV2.Peaks.clsPeakProcessorParameters peakParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(2, 0.75, true, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC);
Task mspeakDet = new DeconToolsPeakDetector(peakParams);
Task theorFeatureGen = new TomTheorFeatureGenerator();
Task targetedFeatureFinder = new BasicTFF(6);
Task exporter = new BasicMTResultSQLiteExporter(cysteineAnalysisOutput1);
IsotopicProfileFitScoreCalculator fitScoreCalc = new IsotopicProfileFitScoreCalculator();
int successCounter = 0;
List <long> timingResults = new List <long>();
foreach (MassTag mt in massTagColl.MassTagList)
{
run.CurrentMassTag = mt;
mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS;
Console.WriteLine();
Console.WriteLine();
Console.WriteLine("------------------- MassTag = " + mt.ID + "---------------------------");
Console.WriteLine("monoMass = " + mt.MonoIsotopicMass.ToString("0.0000") + "; monoMZ = " + mt.MZ.ToString("0.0000") + "; ChargeState = " + mt.ChargeState + "; NET = " + mt.NETVal.ToString("0.000") + "; Sequence = " + mt.PeptideSequence + "\n");
Stopwatch sw = new Stopwatch();
sw.Start();
try
{
peakChromGen.Execute(run.ResultCollection);
smoother.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
chromPeakSel.Execute(run.ResultCollection);
msgen.Execute(run.ResultCollection);
mspeakDet.Execute(run.ResultCollection);
theorFeatureGen.Execute(run.ResultCollection);
targetedFeatureFinder.Execute(run.ResultCollection);
fitScoreCalc.Execute(run.ResultCollection);
MassTagResultBase massTagResult = run.ResultCollection.MassTagResultList[mt];
massTagResult.DisplayToConsole();
Console.WriteLine("------------------------------ end --------------------------");
}
catch (Exception ex)
{
Console.WriteLine("Task failed. Message: " + ex.Message + ex.StackTrace);
}
sw.Stop();
timingResults.Add(sw.ElapsedMilliseconds);
if (mt == massTagColl.MassTagList.Last())
{
exporter.Execute(run.ResultCollection);
}
}
exporter.Cleanup();
//List<IMassTagResult> successfulResults = run.ResultCollection.GetSuccessfulMassTagResults();
foreach (long tr in timingResults)
{
Console.WriteLine(tr);
}
Console.WriteLine("-------- Analysis time for all MTs = " + timingResults.Sum());
Console.WriteLine("-------- Average time for each MT = " + timingResults.Average());
Console.WriteLine();
}
public override void Deconvolute(ResultCollection resultList)
{
float[] xvals = new float[1];
float[] yvals = new float[1];
resultList.Run.XYData.GetXYValuesAsSingles(ref xvals, ref yvals);
int sizeOfRapidArray = 10000;
int[] chargeResults = new int[sizeOfRapidArray];
double[] intensityResults = new double[sizeOfRapidArray];
double[] mzResults = new double[sizeOfRapidArray];
double[] scoreResults = new double[sizeOfRapidArray];
double[] avgmassResults = new double[sizeOfRapidArray];
double[] massResults = new double[sizeOfRapidArray];
double[] mostAbundantMassResults = new double[sizeOfRapidArray];
if (resultList.Run.PeakList == null || resultList.Run.PeakList.Count == 0)
{
return;
}
rapidPeakList = ConvertPeakListToRapidPeakList(resultList.Run.PeakList);
if (rapidPeakList == null || rapidPeakList.Length == 0)
{
return;
}
double rapidsBackgroundIntensityParameter = (resultList.Run.CurrentBackgroundIntensity * minPeptideToBackgroundRatio);
Transformer.PerformTransform_cluster(Convert.ToSingle(rapidsBackgroundIntensityParameter),
ref xvals, ref yvals, ref rapidPeakList, ref chargeResults,
ref intensityResults, ref mzResults, ref scoreResults, ref avgmassResults,
ref massResults, ref mostAbundantMassResults);
GenerateResults(resultList, ref chargeResults, ref intensityResults,
ref mzResults, ref scoreResults,
ref avgmassResults, ref massResults,
ref mostAbundantMassResults, this.resultCombiningMode);
if (this.IsNewFitCalculationPerformed)
{
//HACK: RAPID doesn't return the peaks of the isotopic profile. And it's score is meaningless. So will iterate over
//the results and 1) get the peaks of the isotopic profile and 2) get a least-squares fit of the isotopic profile.
foreach (IsosResult result in resultList.IsosResultBin)
{
//create a temporary mass tag, as a data object for storing relevent info, and using the CalculateMassesForIsotopicProfile() method.
PeptideTarget mt = new PeptideTarget();
mt.ChargeState = (short)result.IsotopicProfile.ChargeState;
mt.MonoIsotopicMass = result.IsotopicProfile.MonoIsotopicMass;
mt.MZ = (mt.MonoIsotopicMass / mt.ChargeState) + Globals.PROTON_MASS;
mt.EmpiricalFormula = _TomIsotopicPatternCreator.GetClosestAvnFormula(result.IsotopicProfile.MonoIsotopicMass, false);
mt.IsotopicProfile = _TomIsotopicPatternCreator.GetIsotopePattern(mt.EmpiricalFormula, _TomIsotopicPatternCreator.aafIsos);
mt.CalculateMassesForIsotopicProfile(mt.ChargeState);
double toleranceInPPM = calcToleranceInPPMFromIsotopicProfile(result.IsotopicProfile);
//this finds the isotopic profile based on the theor. isotopic profile.
BasicTFF bff = new BasicTFF(toleranceInPPM, false);
IsotopicProfile iso = bff.FindMSFeature(resultList.Run.PeakList, mt.IsotopicProfile);
if (iso != null && iso.Peaklist != null && iso.Peaklist.Count > 1)
{
//start at the second peak... and add the newly found peaks
for (int i = 1; i < iso.Peaklist.Count; i++)
{
result.IsotopicProfile.Peaklist.Add(iso.Peaklist[i]);
}
//now that we have the peaks, we can get info for MonoPlusTwoAbundance
result.IsotopicProfile.MonoPlusTwoAbundance = result.IsotopicProfile.GetMonoPlusTwoAbundance();
}
XYData theorXYData = mt.IsotopicProfile.GetTheoreticalIsotopicProfileXYData(result.IsotopicProfile.GetFWHM());
//offset the theor isotopic profile
offsetDistribution(theorXYData, mt.IsotopicProfile, result.IsotopicProfile);
AreaFitter areafitter = new AreaFitter();
int ionCountUsed;
double fitval = areafitter.GetFit(theorXYData, result.Run.XYData, 0.1, out ionCountUsed);
if (fitval == double.NaN || fitval > 1)
{
fitval = 1;
}
result.IsotopicProfile.Score = fitval;
}
}
}
public void test01_mt230140708_z3()
{
double featureFinderTol = 15;
var featureFinderRequiresMonoPeak = false;
var numPeaksUsedInQuant = 3;
var n14n15Util = new N14N15TestingUtilities();
//get MS
var massSpectrum = n14n15Util.GetSpectrumAMTTag23140708_Z3_Sum3(); //this is the diff b/w previous test and this one
var smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.SavitzkyGolaySmoother(3, 2);
massSpectrum = smoother.Smooth(massSpectrum);
//get target MT
var mt23140708 = n14n15Util.CreateMT23140708_Z3();
//get ms peaks
var peakDet = new DeconToolsPeakDetectorV2(1.3, 2, Globals.PeakFitType.QUADRATIC, false);
var msPeakList = peakDet.FindPeaks(massSpectrum, 0, 0);
//TestUtilities.DisplayPeaks(msPeakList);
var featureGen = new TomTheorFeatureGenerator();
featureGen.GenerateTheorFeature(mt23140708);
TestUtilities.DisplayIsotopicProfileData(mt23140708.IsotopicProfile);
var featureGen2 = new JoshTheorFeatureGenerator();
featureGen2.GenerateTheorFeature(mt23140708);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(mt23140708.IsotopicProfile);
var gen = new N15IsotopeProfileGenerator();
var theorN15Profile = gen.GetN15IsotopicProfile(mt23140708, 0.005);
var bff = new BasicTFF(featureFinderTol, featureFinderRequiresMonoPeak);
var n14Profile = bff.FindMSFeature(msPeakList, mt23140708.IsotopicProfile);
var n15Profile = bff.FindMSFeature(msPeakList, theorN15Profile);
Console.WriteLine(mt23140708.GetEmpiricalFormulaFromTargetCode());
TestUtilities.DisplayIsotopicProfileData(mt23140708.IsotopicProfile);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(theorN15Profile);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(n14Profile);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(n15Profile);
var quant = new BasicN14N15Quantifier(featureFinderTol);
double ratioContribIso1;
double ratioContribIso2;
double ratio;
quant.GetRatioBasedOnTopPeaks(n14Profile, n15Profile, mt23140708.IsotopicProfile, theorN15Profile, peakDet.BackgroundIntensity,
numPeaksUsedInQuant, out ratio, out ratioContribIso1, out ratioContribIso2);
Console.WriteLine("--------------------------------");
Console.WriteLine("Background intensity = " + peakDet.BackgroundIntensity);
Console.WriteLine("--------------------------------");
Console.WriteLine("Ratio = " + ratio);
Console.WriteLine("Ratio contrib Iso1 = " + ratioContribIso1);
Console.WriteLine("Ratio contrib Iso2 = " + ratioContribIso2);
Console.WriteLine("--------------------------------");
Assert.AreEqual(1.458267m, (decimal)Math.Round(ratio, 6)); //see 'N14N15Quantification_manualValidation_of_algorithm.xls' for manual validation
}
/// <summary>
/// Executes the cross-link search for LC-IMS-TOF data.
/// </summary>
/// <param name="settings">Settings object to control parameters for cross-linking.</param>
/// <param name="proteinSequenceEnumerable">IEnumerable of protein sequences, as a .NET Bio ISequence object.</param>
/// <param name="featureList">List of LC-IMS-MS Features, as LcImsMsFeature.</param>
/// <param name="peakList">List of Isotopic Peaks, as IsotopicPeak.</param>
/// <returns>An enumerable of CrossLinkResult objects.</returns>
public static IList <CrossLinkResult> Execute(
CrossLinkSettings settings,
IEnumerable <ISequence> proteinSequenceEnumerable,
List <LcImsMsFeature> featureList,
List <IsotopicPeak> peakList)
{
var massToleranceBase = settings.MassTolerance;
var maxMissedCleavages = settings.MaxMissedCleavages;
var digestionRule = settings.TrypticType;
CrossLinkUtil.StaticDeltaMass = settings.StaticDeltaMass;
CrossLinkUtil.UseC13 = settings.UseC13;
CrossLinkUtil.UseN15 = settings.UseN15;
Console.WriteLine();
Console.WriteLine("Mass Tolerance: " + massToleranceBase + " ppm");
Console.WriteLine("Max missed cleavages: " + maxMissedCleavages);
Console.WriteLine("Digestion rule: " + settings.TrypticType);
Console.WriteLine("Delta mass uses C13: " + settings.UseC13);
Console.WriteLine("Delta mass uses N15: " + settings.UseN15);
Console.WriteLine("Static delta mass addon: " + settings.StaticDeltaMass + " Da");
// Used for finding Isotopic Profiles in the data
var msFeatureFinder = new BasicTFF();
var crossLinkList = new List <CrossLink>();
var lastProgress = DateTime.UtcNow;
var proteinsProcessed = 0;
// Create CrossLink objects from all of the protein sequences
foreach (var proteinSequence in proteinSequenceEnumerable)
{
var proteinSequenceString = new string(proteinSequence.Select((a => (char)a)).ToArray());
var proteinId = proteinSequence.ID;
// Get a List of Peptides from the Protein Sequence
var peptideList = SequenceUtil.DigestProtein(proteinSequenceString, digestionRule, maxMissedCleavages);
// Find all possible cross links from the peptide list
var crossLinkEnumerable = CrossLinkUtil.GenerateTheoreticalCrossLinks(peptideList, proteinSequenceString, proteinId);
crossLinkList.AddRange(crossLinkEnumerable);
proteinsProcessed++;
if (DateTime.UtcNow.Subtract(lastProgress).TotalSeconds >= 15)
{
lastProgress = DateTime.UtcNow;
Console.WriteLine("Creating cross linked peptide list; " + proteinsProcessed + " proteins processed");
}
}
Console.WriteLine("Sorting cross-linked peptides");
// Sort the CrossLinks by mass so that the results are ordered in a friendly way
IEnumerable <CrossLink> orderedCrossLinkEnumerable = crossLinkList.OrderBy(x => x.Mass);
// Sort Feature by mass so we can use binary search
featureList = featureList.OrderBy(x => x.MassMonoisotopic).ToList();
// Set up a Feature Comparer and Peak Comparer to use for binary search later on
var featureComparer = new AnonymousComparer <LcImsMsFeature>((x, y) => x.MassMonoisotopic.CompareTo(y.MassMonoisotopic));
var peakComparer = new AnonymousComparer <IsotopicPeak>((x, y) => x.ScanLc != y.ScanLc ? x.ScanLc.CompareTo(y.ScanLc) : x.ScanIms != y.ScanIms ? x.ScanIms.CompareTo(y.ScanIms) : x.Mz.CompareTo(y.Mz));
// Sort the Isotopic Peaks by LC Scan, IMS Scan, and m/z to set them up for binary search later on
peakList.Sort(peakComparer);
var crossLinkResultList = new List <CrossLinkResult>();
var totalCandidatePeptides = crossLinkList.Count;
Console.WriteLine("Searching isotopic data vs. " + totalCandidatePeptides.ToString("#,##0") + " candidate cross-linked peptides");
lastProgress = DateTime.UtcNow;
var crosslinkCandidatesProcessed = 0;
// Search the data for the existence of cross-links
foreach (var crossLink in orderedCrossLinkEnumerable)
{
// Calculate mass tolerance to use for binary search
var massTolerance = massToleranceBase * crossLink.Mass / GeneralConstants.PPM_DIVISOR;
var lowFeature = new LcImsMsFeature {
MassMonoisotopic = crossLink.Mass - massTolerance
};
var highFeature = new LcImsMsFeature {
MassMonoisotopic = crossLink.Mass + massTolerance
};
var lowFeaturePosition = featureList.BinarySearch(lowFeature, featureComparer);
var highFeaturePosition = featureList.BinarySearch(highFeature, featureComparer);
lowFeaturePosition = lowFeaturePosition < 0 ? ~lowFeaturePosition : lowFeaturePosition;
highFeaturePosition = highFeaturePosition < 0 ? ~highFeaturePosition : highFeaturePosition;
// Iterate over all LC-IMS-MS Features that match the Unmodified cross-link mass
for (var i = lowFeaturePosition; i < highFeaturePosition; i++)
{
var feature = featureList[i];
// Search for a mass shift in each of the LC Scans the unmodified cross-link mass was found
for (var currentScanLc = feature.ScanLcStart; currentScanLc <= feature.ScanLcEnd; currentScanLc++)
{
var crossLinkResult = new CrossLinkResult(crossLink, feature, currentScanLc);
var candidatePeaks = PeakUtil.FindCandidatePeaks(peakList, feature.MzMonoisotopic, currentScanLc, feature.ScanImsRep);
var massShiftList = crossLink.MassShiftList;
var shiftedMassList = new List <double>();
// Calculate the shifted mass values that we want to search for
switch (massShiftList.Count)
{
case 1:
{
var firstNewMass = feature.MassMonoisotopic + massShiftList[0];
shiftedMassList.Add(firstNewMass);
}
break;
case 2:
{
var firstNewMass = feature.MassMonoisotopic + massShiftList[0];
var secondNewMass = feature.MassMonoisotopic + massShiftList[1];
var thirdNewMass = feature.MassMonoisotopic + massShiftList[0] + massShiftList[1];
shiftedMassList.Add(firstNewMass);
shiftedMassList.Add(secondNewMass);
shiftedMassList.Add(thirdNewMass);
}
break;
}
// Search for shifted mass values in Isotopic Peaks
foreach (var shiftedMass in shiftedMassList)
{
var shiftedMz = (shiftedMass / feature.ChargeState) + GeneralConstants.MASS_OF_PROTON;
// Create theoretical Isotopic Peaks that will later form a theoretical Isotopic Profile
var theoreticalPeakList = new List <MSPeak> {
new MSPeak {
XValue = shiftedMz, Height = 1
}
};
for (double k = 1; k < 4; k++)
{
theoreticalPeakList.Add(new MSPeak {
XValue = shiftedMz + (k * 1.003 / feature.ChargeState), Height = (float)(1.0 - (k / 4))
});
theoreticalPeakList.Add(new MSPeak {
XValue = shiftedMz - (k * 1.003 / feature.ChargeState), Height = (float)(1.0 - (k / 4))
});
}
// Sort peaks by m/z
var sortPeaksQuery = from peak in theoreticalPeakList
orderby peak.XValue
select peak;
// Create a theoretical Isotopic Profile for DeconTools to search for
var isotopicProfile = new IsotopicProfile
{
MonoIsotopicMass = shiftedMass,
MonoPeakMZ = shiftedMz,
ChargeState = feature.ChargeState,
Peaklist = sortPeaksQuery.ToList()
};
// Search for the theoretical Isotopic Profile
var foundProfile = msFeatureFinder.FindMSFeature(candidatePeaks, isotopicProfile, massToleranceBase, false);
/*
* It is possible that the set mono pass of the previous theoretical distribution was the right-most peak of the actual distribution
* If so, we should be able to shift the theoretical distribution over to the left and find the actual distribution
*/
if (foundProfile == null)
{
foreach (var msPeak in sortPeaksQuery)
{
msPeak.XValue -= (1.003 / feature.ChargeState);
}
isotopicProfile = new IsotopicProfile
{
MonoIsotopicMass = shiftedMass - 1.003,
MonoPeakMZ = shiftedMz - (1.003 / feature.ChargeState),
ChargeState = feature.ChargeState,
Peaklist = sortPeaksQuery.ToList()
};
foundProfile = msFeatureFinder.FindMSFeature(candidatePeaks, isotopicProfile, massToleranceBase, false);
}
// Add to results, even if we did not find it.
var didFindProfile = foundProfile != null;
crossLinkResult.MassShiftResults.KvpList.Add(new KeyValuePair <double, bool>(shiftedMass, didFindProfile));
}
crossLinkResultList.Add(crossLinkResult);
}
}
crosslinkCandidatesProcessed++;
if (DateTime.UtcNow.Subtract(lastProgress).TotalSeconds >= 10)
{
lastProgress = DateTime.UtcNow;
var percentComplete = crosslinkCandidatesProcessed / (double)totalCandidatePeptides * 100;
Console.WriteLine("Searching isotopic data; " + percentComplete.ToString("0.0") + "% complete");
}
}
return(crossLinkResultList);
}
/// <summary>
/// Executes the cross-link search for LC-IMS-TOF data.
/// </summary>
/// <param name="settings">Settings object to control parameters for cross-linking.</param>
/// <param name="proteinSequenceEnumerable">IEnumerable of protein sequences, as a .NET Bio ISequence object.</param>
/// <param name="featureList">List of LC-IMS-MS Features, as LcImsMsFeature.</param>
/// <param name="peakList">List of Isotopic Peaks, as IsotopicPeak.</param>
/// <returns>An enumerable of CrossLinkResult objects.</returns>
public static IList<CrossLinkResult> Execute(
CrossLinkSettings settings,
IEnumerable<ISequence> proteinSequenceEnumerable,
List<LcImsMsFeature> featureList,
List<IsotopicPeak> peakList)
{
var massToleranceBase = settings.MassTolerance;
var maxMissedCleavages = settings.MaxMissedCleavages;
var digestionRule = settings.TrypticType;
CrossLinkUtil.StaticDeltaMass = settings.StaticDeltaMass;
CrossLinkUtil.UseC13 = settings.UseC13;
CrossLinkUtil.UseN15 = settings.UseN15;
Console.WriteLine();
Console.WriteLine("Mass Tolerance: " + massToleranceBase + " ppm");
Console.WriteLine("Max missed cleavages: " + maxMissedCleavages);
Console.WriteLine("Digestion rule: " + settings.TrypticType );
Console.WriteLine("Delta mass uses C13: " + settings.UseC13);
Console.WriteLine("Delta mass uses N15: " + settings.UseN15);
Console.WriteLine("Static delta mass addon: " + settings.StaticDeltaMass + " Da");
// Used for finding Isotopic Profiles in the data
var msFeatureFinder = new BasicTFF();
var crossLinkList = new List<CrossLink>();
var lastProgress = DateTime.UtcNow;
var proteinsProcessed = 0;
// Create CrossLink objects from all of the protein sequences
foreach (var proteinSequence in proteinSequenceEnumerable)
{
var proteinSequenceString = new string(proteinSequence.Select((a => (char)a)).ToArray());
var proteinId = proteinSequence.ID;
// Get a List of Peptides from the Protein Sequence
var peptideList = SequenceUtil.DigestProtein(proteinSequenceString, digestionRule, maxMissedCleavages);
// Find all possible cross links from the peptide list
var crossLinkEnumerable = CrossLinkUtil.GenerateTheoreticalCrossLinks(peptideList, proteinSequenceString, proteinId);
crossLinkList.AddRange(crossLinkEnumerable);
proteinsProcessed++;
if (DateTime.UtcNow.Subtract(lastProgress).TotalSeconds >= 15)
{
lastProgress = DateTime.UtcNow;
Console.WriteLine("Creating cross linked peptide list; " + proteinsProcessed + " proteins processed");
}
}
Console.WriteLine("Sorting cross-linked peptides");
// Sort the CrossLinks by mass so that the results are ordered in a friendly way
IEnumerable<CrossLink> orderedCrossLinkEnumerable = crossLinkList.OrderBy(x => x.Mass);
// Sort Feature by mass so we can use binary search
featureList = featureList.OrderBy(x => x.MassMonoisotopic).ToList();
// Set up a Feature Comparer and Peak Comparer to use for binary search later on
var featureComparer = new AnonymousComparer<LcImsMsFeature>((x, y) => x.MassMonoisotopic.CompareTo(y.MassMonoisotopic));
var peakComparer = new AnonymousComparer<IsotopicPeak>((x, y) => x.ScanLc != y.ScanLc ? x.ScanLc.CompareTo(y.ScanLc) : x.ScanIms != y.ScanIms ? x.ScanIms.CompareTo(y.ScanIms) : x.Mz.CompareTo(y.Mz));
// Sort the Isotopic Peaks by LC Scan, IMS Scan, and m/z to set them up for binary search later on
peakList.Sort(peakComparer);
var crossLinkResultList = new List<CrossLinkResult>();
var totalCandidatePeptides = crossLinkList.Count;
Console.WriteLine("Searching isotopic data vs. " + totalCandidatePeptides.ToString("#,##0") + " candidate cross-linked peptides");
lastProgress = DateTime.UtcNow;
var crosslinkCandidatesProcessed = 0;
// Search the data for the existence of cross-links
foreach (var crossLink in orderedCrossLinkEnumerable)
{
// Calculate mass tolerance to use for binary search
var massTolerance = massToleranceBase * crossLink.Mass / GeneralConstants.PPM_DIVISOR;
var lowFeature = new LcImsMsFeature { MassMonoisotopic = crossLink.Mass - massTolerance };
var highFeature = new LcImsMsFeature { MassMonoisotopic = crossLink.Mass + massTolerance };
var lowFeaturePosition = featureList.BinarySearch(lowFeature, featureComparer);
var highFeaturePosition = featureList.BinarySearch(highFeature, featureComparer);
lowFeaturePosition = lowFeaturePosition < 0 ? ~lowFeaturePosition : lowFeaturePosition;
highFeaturePosition = highFeaturePosition < 0 ? ~highFeaturePosition : highFeaturePosition;
// Iterate over all LC-IMS-MS Features that match the Unmodified cross-link mass
for (var i = lowFeaturePosition; i < highFeaturePosition; i++)
{
var feature = featureList[i];
// Search for a mass shift in each of the LC Scans the unmodified cross-link mass was found
for (var currentScanLc = feature.ScanLcStart; currentScanLc <= feature.ScanLcEnd; currentScanLc++)
{
var crossLinkResult = new CrossLinkResult(crossLink, feature, currentScanLc);
var candidatePeaks = PeakUtil.FindCandidatePeaks(peakList, feature.MzMonoisotopic, currentScanLc, feature.ScanImsRep);
var massShiftList = crossLink.MassShiftList;
var shiftedMassList = new List<double>();
// Calculate the shifted mass values that we want to search for
switch (massShiftList.Count)
{
case 1:
{
var firstNewMass = feature.MassMonoisotopic + massShiftList[0];
shiftedMassList.Add(firstNewMass);
}
break;
case 2:
{
var firstNewMass = feature.MassMonoisotopic + massShiftList[0];
var secondNewMass = feature.MassMonoisotopic + massShiftList[1];
var thirdNewMass = feature.MassMonoisotopic + massShiftList[0] + massShiftList[1];
shiftedMassList.Add(firstNewMass);
shiftedMassList.Add(secondNewMass);
shiftedMassList.Add(thirdNewMass);
}
break;
}
// Search for shifted mass values in Isotopic Peaks
foreach (var shiftedMass in shiftedMassList)
{
var shiftedMz = (shiftedMass / feature.ChargeState) + GeneralConstants.MASS_OF_PROTON;
// Create theoretical Isotopic Peaks that will later form a theoretical Isotopic Profile
var theoreticalPeakList = new List<MSPeak> { new MSPeak { XValue = shiftedMz, Height = 1 } };
for (double k = 1; k < 4; k++)
{
theoreticalPeakList.Add(new MSPeak { XValue = shiftedMz + (k * 1.003 / feature.ChargeState), Height = (float)(1.0 - (k / 4)) });
theoreticalPeakList.Add(new MSPeak { XValue = shiftedMz - (k * 1.003 / feature.ChargeState), Height = (float)(1.0 - (k / 4)) });
}
// Sort peaks by m/z
var sortPeaksQuery = from peak in theoreticalPeakList
orderby peak.XValue
select peak;
// Create a theoretical Isotopic Profile for DeconTools to search for
var isotopicProfile = new IsotopicProfile
{
MonoIsotopicMass = shiftedMass,
MonoPeakMZ = shiftedMz,
ChargeState = feature.ChargeState,
Peaklist = sortPeaksQuery.ToList()
};
// Search for the theoretical Isotopic Profile
var foundProfile = msFeatureFinder.FindMSFeature(candidatePeaks, isotopicProfile, massToleranceBase, false);
/*
* It is possible that the set mono pass of the previous theoretical distribution was the right-most peak of the actual distribution
* If so, we should be able to shift the theoretical distribution over to the left and find the actual distribution
*/
if (foundProfile == null)
{
foreach (var msPeak in sortPeaksQuery)
{
msPeak.XValue -= (1.003 / feature.ChargeState);
}
isotopicProfile = new IsotopicProfile
{
MonoIsotopicMass = shiftedMass - 1.003,
MonoPeakMZ = shiftedMz - (1.003 / feature.ChargeState),
ChargeState = feature.ChargeState,
Peaklist = sortPeaksQuery.ToList()
};
foundProfile = msFeatureFinder.FindMSFeature(candidatePeaks, isotopicProfile, massToleranceBase, false);
}
// Add to results, even if we did not find it.
var didFindProfile = foundProfile != null;
crossLinkResult.MassShiftResults.KvpList.Add(new KeyValuePair<double, bool>(shiftedMass, didFindProfile));
}
crossLinkResultList.Add(crossLinkResult);
}
}
crosslinkCandidatesProcessed++;
if (DateTime.UtcNow.Subtract(lastProgress).TotalSeconds >= 10)
{
lastProgress = DateTime.UtcNow;
var percentComplete = crosslinkCandidatesProcessed / (double)totalCandidatePeptides * 100;
Console.WriteLine("Searching isotopic data; " + percentComplete.ToString("0.0") + "% complete");
}
}
return crossLinkResultList;
}
