public static void TestAddCompIonsClassic()
{
var myMsDataFile = new TestDataFile();
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var proteinList = new List <Protein> {
new Protein("QXQ", null)
};
var productMassTolerance = new AbsoluteTolerance(0.01);
var searchModes = new OpenSearchMode();
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
List <DigestionMotif> motifs = new List <DigestionMotif> {
new DigestionMotif("K", null, 1, null)
};
Protease protease = new Protease("Custom Protease3", CleavageSpecificity.Full, null, null, motifs);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
CommonParameters CommonParameters = new CommonParameters(
digestionParams: new DigestionParams(protease: protease.Name, maxMissedCleavages: 0, minPeptideLength: 1),
scoreCutoff: 1,
addCompIons: false);
var fsp = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp.Add(("", CommonParameters));
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchModes, CommonParameters, fsp, null, new List <string>()).Run();
CommonParameters CommonParameters2 = new CommonParameters(
digestionParams: new DigestionParams(protease: protease.Name, maxMissedCleavages: 0, minPeptideLength: 1),
scoreCutoff: 1,
addCompIons: true);
var fsp2 = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp2.Add(("", CommonParameters2));
PeptideSpectralMatch[] allPsmsArray2 = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray2, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchModes, CommonParameters2, fsp2, null, new List <string>()).Run();
double scoreT = allPsmsArray2[0].Score;
double scoreF = allPsmsArray[0].Score;
// Single search mode
Assert.AreEqual(allPsmsArray.Length, allPsmsArray2.Length);
// Single ms2 scan
Assert.AreEqual(allPsmsArray.Length, allPsmsArray2.Length);
Assert.IsTrue(scoreT > 1);
Assert.AreEqual(allPsmsArray[0].ScanNumber, allPsmsArray2[0].ScanNumber);
Assert.IsTrue(scoreT == scoreF * 3 && scoreT > scoreF + 2);
}
public static void TestAddCompIonsClassic()
{
var myMsDataFile = new TestDataFile();
var variableModifications = new List <ModificationWithMass>();
var fixedModifications = new List <ModificationWithMass>();
var proteinList = new List <Protein> {
new Protein("QXQ", null)
};
var productMassTolerance = new AbsoluteTolerance(0.01);
var searchModes = new OpenSearchMode();
bool DoPrecursorDeconvolution = true;
bool UseProvidedPrecursorInfo = true;
double DeconvolutionIntensityRatio = 4;
int DeconvolutionMaxAssumedChargeState = 10;
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, DoPrecursorDeconvolution, UseProvidedPrecursorInfo, DeconvolutionIntensityRatio, DeconvolutionMaxAssumedChargeState, DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
CommonParameters CommonParameters = new CommonParameters
{
DigestionParams = new DigestionParams
{
Protease = new Protease("Custom Protease", new List <string> {
"K"
}, new List <string>(), TerminusType.C, CleavageSpecificity.Full, null, null, null),
MinPeptideLength = null,
MaxMissedCleavages = 0
},
ConserveMemory = false,
ScoreCutoff = 1,
};
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, proteinList, new List <ProductType> {
ProductType.B, ProductType.Y
}, searchModes, false, CommonParameters, CommonParameters.ProductMassTolerance, new List <string>()).Run();
PeptideSpectralMatch[] allPsmsArray2 = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray2, listOfSortedms2Scans, variableModifications, fixedModifications, proteinList, new List <ProductType> {
ProductType.B, ProductType.Y
}, searchModes, true, CommonParameters, CommonParameters.ProductMassTolerance, new List <string>()).Run();
double scoreT = allPsmsArray2[0].Score;
double scoreF = allPsmsArray[0].Score;
// Single search mode
Assert.AreEqual(allPsmsArray.Length, allPsmsArray2.Length);
// Single ms2 scan
Assert.AreEqual(allPsmsArray.Length, allPsmsArray2.Length);
Assert.IsTrue(scoreT > 1);
Assert.AreEqual(allPsmsArray[0].ScanNumber, allPsmsArray2[0].ScanNumber);
Assert.IsTrue(scoreT == scoreF * 3 && scoreT > scoreF + 2);
}
private static MassDiffAcceptor ParseSearchMode(string text)
{
MassDiffAcceptor massDiffAcceptor = null;
try
{
var split = text.Split(' ');
switch (split[1])
{
case "dot":
double[] massShifts = split[4].Split(',').Select(p => double.Parse(p, CultureInfo.InvariantCulture)).ToArray();
string newString = split[2].Replace("�", "");
double toleranceValue = double.Parse(newString, CultureInfo.InvariantCulture);
if (split[3].ToUpperInvariant().Equals("PPM"))
{
massDiffAcceptor = new DotMassDiffAcceptor(split[0], massShifts, new PpmTolerance(toleranceValue));
}
else if (split[3].ToUpperInvariant().Equals("DA"))
{
massDiffAcceptor = new DotMassDiffAcceptor(split[0], massShifts, new AbsoluteTolerance(toleranceValue));
}
break;
case "interval":
IEnumerable <DoubleRange> doubleRanges = Array.ConvertAll(split[2].Split(';'), b => new DoubleRange(double.Parse(b.Trim(new char[] { '[', ']' }).Split(',')[0],
CultureInfo.InvariantCulture), double.Parse(b.Trim(new char[] { '[', ']' }).Split(',')[1], CultureInfo.InvariantCulture)));
massDiffAcceptor = new IntervalMassDiffAcceptor(split[0], doubleRanges);
break;
case "OpenSearch":
massDiffAcceptor = new OpenSearchMode();
break;
case "daltonsAroundZero":
massDiffAcceptor = new SingleAbsoluteAroundZeroSearchMode(double.Parse(split[2], CultureInfo.InvariantCulture));
break;
case "ppmAroundZero":
massDiffAcceptor = new SinglePpmAroundZeroSearchMode(double.Parse(split[2], CultureInfo.InvariantCulture));
break;
default:
throw new MetaMorpheusException("Unrecognized search mode type: " + split[1]);
}
}
catch (Exception e)
{
throw new MetaMorpheusException("Could not parse search mode string: " + e.Message);
}
return(massDiffAcceptor);
}
private static MassDiffAcceptor ParseSearchMode(string text)
{
MassDiffAcceptor ye = null;
var split = text.Split(' ');
switch (split[1])
{
case "dot":
var massShifts = Array.ConvertAll(split[4].Split(','), Double.Parse);
var newString = split[2].Replace("�", "");
var toleranceValue = double.Parse(newString, CultureInfo.InvariantCulture);
if (split[3].ToUpperInvariant().Equals("PPM"))
{
ye = new DotMassDiffAcceptor(split[0], massShifts, new PpmTolerance(toleranceValue));
}
else if (split[3].ToUpperInvariant().Equals("DA"))
{
ye = new DotMassDiffAcceptor(split[0], massShifts, new AbsoluteTolerance(toleranceValue));
}
break;
case "interval":
IEnumerable <DoubleRange> doubleRanges = Array.ConvertAll(split[2].Split(','), b => new DoubleRange(double.Parse(b.Trim(new char[] { '[', ']' }).Split(';')[0], CultureInfo.InvariantCulture), double.Parse(b.Trim(new char[] { '[', ']' }).Split(';')[1], CultureInfo.InvariantCulture)));
ye = new IntervalMassDiffAcceptor(split[0], doubleRanges);
break;
case "OpenSearch":
ye = new OpenSearchMode();
break;
case "daltonsAroundZero":
ye = new SingleAbsoluteAroundZeroSearchMode(double.Parse(split[2], CultureInfo.InvariantCulture));
break;
case "ppmAroundZero":
ye = new SinglePpmAroundZeroSearchMode(double.Parse(split[2], CultureInfo.InvariantCulture));
break;
default:
throw new MetaMorpheusException("Could not parse search mode string");
}
return(ye);
}
public static void TestMatchIonsOfAllChargesBottomUp()
{
CommonParameters CommonParameters = new CommonParameters();
MetaMorpheusTask.DetermineAnalyteType(CommonParameters);
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var proteinList = new List <Protein>
{
new Protein("AAAHSSLK", ""), new Protein("RQPAQPR", ""), new Protein("EKAEAEAEK", "")
};
var myMsDataFile = Mzml.LoadAllStaticData(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SmallCalibratible_Yeast.mzML"));
var searchMode = new SinglePpmAroundZeroSearchMode(5);
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
//search by new method of looking for all charges
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchMode, CommonParameters, null, null, new List <string>(), true).Run();
var psm = allPsmsArray.Where(p => p != null).ToList();
Assert.That(psm[1].MatchedFragmentIons.Count == 14);
//there are ions with same product type and same fragment number but different charges
Assert.That(psm[1].MatchedFragmentIons[8].NeutralTheoreticalProduct.ProductType == psm[1].MatchedFragmentIons[9].NeutralTheoreticalProduct.ProductType &&
psm[1].MatchedFragmentIons[8].NeutralTheoreticalProduct.FragmentNumber == psm[1].MatchedFragmentIons[9].NeutralTheoreticalProduct.FragmentNumber &&
psm[1].MatchedFragmentIons[8].Charge != psm[1].MatchedFragmentIons[9].Charge);
Assert.That(psm[2].MatchedFragmentIons.Count == 14);
Assert.That(psm[4].MatchedFragmentIons.Count == 16);
//search by old method of looking for only one charge
PeptideSpectralMatch[] allPsmsArray_oneCharge = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray_oneCharge, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchMode, CommonParameters, null, null, new List <string>(), false).Run();
var psm_oneCharge = allPsmsArray_oneCharge.Where(p => p != null).ToList();
//compare 2 scores , they should have same integer part but new search has a little higher score than old search
Assert.That(psm[1].Score > psm_oneCharge[1].Score);
Assert.AreEqual(Math.Truncate(psm[1].Score), 12);
Assert.AreEqual(Math.Truncate(psm_oneCharge[1].Score), 12);
//compare 2 results and evaluate the different matched ions
var peptideTheorProducts = new List <Product>();
Assert.That(psm_oneCharge[1].MatchedFragmentIons.Count == 12);
var differences = psm[1].MatchedFragmentIons.Except(psm_oneCharge[1].MatchedFragmentIons);
psm[1].BestMatchingPeptides.First().Peptide.Fragment(CommonParameters.DissociationType, CommonParameters.DigestionParams.FragmentationTerminus, peptideTheorProducts);
foreach (var ion in differences)
{
foreach (var product in peptideTheorProducts)
{
if (product.Annotation.ToString().Equals(ion.NeutralTheoreticalProduct.Annotation.ToString()))
{
//to see if the different matched ions are qualified
Assert.That(CommonParameters.ProductMassTolerance.Within(ion.Mz.ToMass(ion.Charge), product.NeutralMass));
}
}
}
//test specific condition: unknown fragment mass; this only happens rarely for sequences with unknown amino acids
var myMsDataFile1 = new TestDataFile();
var variableModifications1 = new List <Modification>();
var fixedModifications1 = new List <Modification>();
var proteinList1 = new List <Protein> {
new Protein("QXQ", null)
};
var productMassTolerance = new AbsoluteTolerance(0.01);
var searchModes = new OpenSearchMode();
Tolerance DeconvolutionMassTolerance1 = new PpmTolerance(5);
var listOfSortedms2Scans1 = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
List <DigestionMotif> motifs = new List <DigestionMotif> {
new DigestionMotif("K", null, 1, null)
};
Protease protease = new Protease("Custom Protease3", CleavageSpecificity.Full, null, null, motifs);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
CommonParameters CommonParameters1 = new CommonParameters(
digestionParams: new DigestionParams(protease: protease.Name, maxMissedCleavages: 0, minPeptideLength: 1),
scoreCutoff: 1,
addCompIons: false);
var fsp = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp.Add(("", CommonParameters));
PeptideSpectralMatch[] allPsmsArray1 = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
bool writeSpectralLibrary = true;
new ClassicSearchEngine(allPsmsArray1, listOfSortedms2Scans1, variableModifications1, fixedModifications1, null, null, null,
proteinList1, searchModes, CommonParameters1, fsp, null, new List <string>(), writeSpectralLibrary).Run();
var psm1 = allPsmsArray1.Where(p => p != null).ToList();
Assert.AreEqual(psm1.Count, 222);
}
protected override MetaMorpheusEngineResults RunSpecific()
{
MassDiffAcceptor XLsearchMode = new OpenSearchMode();
CrosslinkAnalysisResults myAnalysisResults = new CrosslinkAnalysisResults(this);
Status("Running analysis engine!");
//At this point have Spectrum-Sequence matching, without knowing which protein, and without know if target/decoy
#region Match Seqeunces to PeptideWithSetModifications
//myAnalysisResults.AddText("Starting compactPeptideToProteinPeptideMatching count: " + compactPeptideToProteinPeptideMatching.Count);
Status("Adding observed peptides to dictionary...");
foreach (var psmpair in newPsms)
{
if (psmpair != null)
{
var cp = psmpair.compactPeptide;
if (!compactPeptideToProteinPeptideMatching.ContainsKey(cp))
{
compactPeptideToProteinPeptideMatching.Add(cp, new HashSet <PeptideWithSetModifications>());
}
if (psmpair.BetaPsmCross != null)
{
var cp1 = psmpair.BetaPsmCross.compactPeptide;
if (!compactPeptideToProteinPeptideMatching.ContainsKey(cp1))
{
compactPeptideToProteinPeptideMatching.Add(cp1, new HashSet <PeptideWithSetModifications>());
}
}
}
}
//myAnalysisResults.AddText("Ending compactPeptideToProteinPeptideMatching count: " + compactPeptideToProteinPeptideMatching.Count);
int totalProteins = proteinList.Count;
int proteinsSeen = 0;
int old_progress = 0;
var obj = new object();
Status("Adding possible sources to peptide dictionary...");
Parallel.ForEach(Partitioner.Create(0, totalProteins), fff =>
{
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > local = compactPeptideToProteinPeptideMatching.ToDictionary(b => b.Key, b => new HashSet <PeptideWithSetModifications>());
for (int i = fff.Item1; i < fff.Item2; i++)
{
foreach (var peptideWithSetModifications in proteinList[i].Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications))
{
if (local.TryGetValue(new CompactPeptide(peptideWithSetModifications, terminusType), out HashSet <PeptideWithSetModifications> v))
{
v.Add(peptideWithSetModifications);
}
}
}
lock (obj)
{
foreach (var ye in local)
{
if (compactPeptideToProteinPeptideMatching.TryGetValue(ye.Key, out HashSet <PeptideWithSetModifications> v))
{
foreach (var huh in ye.Value)
{
v.Add(huh);
}
}
}
proteinsSeen += fff.Item2 - fff.Item1;
var new_progress = (int)((double)proteinsSeen / (totalProteins) * 100);
if (new_progress > old_progress)
{
ReportProgress(new ProgressEventArgs(new_progress, "In adding possible" +
" sources to peptide dictionary loop", nestedIds));
old_progress = new_progress;
}
}
});
#endregion Match Seqeunces to PeptideWithSetModifications
Status("Computing info about actual peptides with modifications...");
for (int myScanWithMassIndex = 0; myScanWithMassIndex < newPsms.Count; myScanWithMassIndex++)
{
var huh = newPsms[myScanWithMassIndex];
if (huh != null)
{
huh.MatchToProteinLinkedPeptides(compactPeptideToProteinPeptideMatching);
}
if (huh != null)
{
var huh1 = newPsms[myScanWithMassIndex].BetaPsmCross;
if (huh1 != null)
{
huh1.MatchToProteinLinkedPeptides(compactPeptideToProteinPeptideMatching);
}
}
}
return(myAnalysisResults);
}
