public static void AnnotateModifications(PsmFromTsv spectrumMatch, Canvas sequenceDrawingCanvas, string fullSequence, int yLoc, double?spacer = null, int xShift = 12)
{
var peptide = new PeptideWithSetModifications(fullSequence, GlobalVariables.AllModsKnownDictionary);
// read glycans if applicable
List <Tuple <int, string, double> > localGlycans = null;
if (spectrumMatch.GlycanLocalizationLevel != null)
{
localGlycans = PsmFromTsv.ReadLocalizedGlycan(spectrumMatch.LocalizedGlycan);
}
// annotate mods
foreach (var mod in peptide.AllModsOneIsNterminus)
{
double xLocation = (mod.Key - 1) * (spacer ?? MetaDrawSettings.AnnotatedSequenceTextSpacing) - xShift;
double yLocation = yLoc + 2;
if (mod.Value.ModificationType == "O-Glycosylation")
{
if (localGlycans.Where(p => p.Item1 + 1 == mod.Key).Count() > 0)
{
DrawCircle(sequenceDrawingCanvas, new Point(xLocation, yLocation), MetaDrawSettings.ModificationAnnotationColor);
}
else
{
DrawCircle(sequenceDrawingCanvas, new Point(xLocation, yLocation), Brushes.Gray);
}
}
else
{
DrawCircle(sequenceDrawingCanvas, new Point(xLocation, yLocation), MetaDrawSettings.ModificationAnnotationColor);
}
}
}
public static void GlyTest_ModificationSites()
{
PeptideWithSetModifications pep = new PeptideWithSetModifications("ELNPTPNVEVNVECR", null);
string[] motifs = new string[] { "Nxs", "Nxt" };
var sites = GlycoSpectralMatch.GetPossibleModSites(pep, motifs);
Assert.That(sites.Count() == 1 && sites[0] == 4);
ModificationMotif.TryGetMotif("C", out ModificationMotif motif1);
Modification mod1 = new Modification(_originalId: "Carbamidomethyl of C", _modificationType: "Common Fixed", _target: motif1, _locationRestriction: "Anywhere.", _monoisotopicMass: 57.02146372068994);
ModificationMotif.TryGetMotif("N", out ModificationMotif motif2);
Modification mod2 = new Modification(_originalId: "Test of N", _modificationType: "Common Fixed", _target: motif2, _locationRestriction: "Anywhere.");
var testN = new PeptideWithSetModifications("C[Common Fixed:Carbamidomethyl of C]N[Common Fixed:Test of N]SSDQPKL[Common Fixed:Carbamidomethyl of C]NLSGIETP", new Dictionary <string, Modification> {
{ "Carbamidomethyl of C", mod1 }, { "Test of N", mod2 }
});
var testSites = GlycoSpectralMatch.GetPossibleModSites(testN, motifs);
Assert.That(testSites.Count() == 1 && testSites[0] == 11);
var testC = new PeptideWithSetModifications("TELAAYLSC[Common Fixed:Carbamidomethyl of C]NATK", new Dictionary <string, Modification> {
{ "Carbamidomethyl of C", mod1 }
});
var testCSites = GlycoSpectralMatch.GetPossibleModSites(testC, motifs);
Assert.That(testCSites.Count() == 1 && testSites[0] == 11);
}
public static void TestHardToParseModifiedSequence()
{
string fullSequence = "PE[Metal:Cation:Fe[III] on X]PTIDE";
ModificationMotif.TryGetMotif("X", out var motif);
Modification mod = new Modification(_originalId: "Cation:Fe[III]", _modificationType: "Metal",
_monoisotopicMass: 1, _locationRestriction: "Anywhere.", _target: motif);
Dictionary <string, Modification> mods = new Dictionary <string, Modification> {
{ "Cation:Fe[III] on X", mod }
};
PeptideWithSetModifications pep = new PeptideWithSetModifications(fullSequence, mods);
Assert.That(pep.AllModsOneIsNterminus.Count == 1);
var annotatedMod = pep.AllModsOneIsNterminus.First();
Assert.That(annotatedMod.Key == 3);
Assert.That(annotatedMod.Value.IdWithMotif == "Cation:Fe[III] on X");
Assert.That(annotatedMod.Value.OriginalId == "Cation:Fe[III]");
Assert.That(annotatedMod.Value.ModificationType == "Metal");
fullSequence = "[Metal:Cation:Fe[III] on X]PE[Metal:Cation:Fe[III] on X]PTIDE[Metal:Cation:Fe[III] on X]";
pep = new PeptideWithSetModifications(fullSequence, mods);
Assert.That(pep.AllModsOneIsNterminus.Count == 3);
Assert.That(pep.AllModsOneIsNterminus.Keys.ToList().SequenceEqual(new int[] { 1, 3, 8 }));
}
public static void TestCompactPeptideSerialization()
{
// purpose of this test is to serialize/deserialize a CompactPeptide and make sure the deserialized peptide
// has the same properties as before it was serialized. This peptide is unmodified
string sequence = "PEPTIDE";
PeptideWithSetModifications p = new PeptideWithSetModifications(sequence, new Dictionary <string, Modification>(), 0, null, null, 0, 7, 0, null);
CompactPeptide cp = p.CompactPeptide(FragmentationTerminus.Both);
CompactPeptide deserializedCp = null;
string dir = System.IO.Path.Combine(TestContext.CurrentContext.TestDirectory, "TestCompactPeptideSerialization");
System.IO.Directory.CreateDirectory(dir);
string path = System.IO.Path.Combine(dir, "myCompactPeptideIndex.ind");
var messageTypes = typeof(CompactPeptide);
var ser = new NetSerializer.Serializer(new List <Type> {
messageTypes
});
using (var file = System.IO.File.Create(path))
{
ser.Serialize(file, cp);
}
using (var file = System.IO.File.OpenRead(path))
{
deserializedCp = (CompactPeptide)ser.Deserialize(file);
}
Assert.That(cp.Equals(deserializedCp));
}
public void CZE_RetentionTime_Test()
{
CZE testCZE = new CZE(1, 1);
double expElutionTime = 1;
double expMu = Math.Round(testCZE.ExperimentalElectrophoreticMobility(expElutionTime), 0);
Assert.AreEqual(expMu, 16666667);
double theoreticalElutionTime = testCZE.TheoreticalElutionTime(expMu);
Assert.AreEqual(Math.Round(expElutionTime, 5), Math.Round(theoreticalElutionTime, 5));
for (int i = 0; i < _peptidesCZE.GetLength(0); i++)
{
var peptide = new PeptideWithSetModifications((string)_peptidesCZE[i, 0], new Dictionary <string, Modification>());
object obj = _peptidesCZE[i, 1];
double expected = (double)_peptidesCZE[i, 1];
double actual = CZE.PredictedElectrophoreticMobility(peptide.BaseSequence, peptide.MonoisotopicMass);
// Round the returned value to match the values presented
// in the supporting information of the SSRCalc 3 publication.
// First cast to float, since the added precision of the double
// caused the double representation of 12.805 to round to 12.80
// instead of 12.81. When diffed with 12.81 the result was
// 0.005000000000002558.
double actualRound = Math.Round((float)actual, 2);
// Extra conditional added to improve debugging of issues.
if (Math.Abs(expected - actual) > 0.005)
{
Assert.AreEqual(expected, actualRound, "Peptide {0}", peptide);
}
}
}
public static void TestContaminantAmbiguity()
{
//create an ms file and a database for the peptide
Protein targetProtein = new Protein("PEPTIDE", "target");
string xmlName = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\PEPTIDE.xml");
ProteinDbWriter.WriteXmlDatabase(null, new List <Protein> {
targetProtein
}, xmlName);
PeptideWithSetModifications pepWithSetMods = targetProtein.Digest(new DigestionParams(), null, null).First();
TestDataFile msFile = new TestDataFile(pepWithSetMods);
string mzmlName = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\PEPTIDE.mzML");
IO.MzML.MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(msFile, mzmlName, false);
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestContaminantAmbiguityOutput");
//run a full modern search using two databases (the same database) but one is called a target and the other is called a contaminant
//KEEP BOTH TARGET AND CONTAMINANT
SearchParameters modernSearchParams = new SearchParameters();
modernSearchParams.SearchType = SearchType.Modern;
modernSearchParams.TCAmbiguity = TargetContaminantAmbiguity.RenameProtein;
SearchTask modernTask = new SearchTask();
modernTask.SearchParameters = modernSearchParams;
EverythingRunnerEngine engine = new EverythingRunnerEngine(new List <(string, MetaMorpheusTask)> {
("task1", modernTask)
}, new List <string> {
public TestDataFile(PeptideWithSetModifications pepWithSetMods)
: base(2, new SourceFile(@"no nativeID format", "mzML format", null, "SHA-1", @"C:\fake.mzML", null))
{
var mz1 = new double[] { pepWithSetMods.MonoisotopicMass.ToMz(2), (pepWithSetMods.MonoisotopicMass + Constants.C13MinusC12).ToMz(2), (pepWithSetMods.MonoisotopicMass + 2 * Constants.C13MinusC12).ToMz(2) };
var intensities1 = new double[] { 1, 1, 1 };
var MassSpectrum1 = new MzSpectrum(mz1, intensities1, false);
var ScansHere = new List <MsDataScan> {
new MsDataScan(MassSpectrum1, 1, 1, true, Polarity.Positive, 1, new MzLibUtil.MzRange(0, 10000), "ff", MZAnalyzerType.Unknown, 1000, 1, null, "scan=1")
};
List <double> mz2 = new List <double>();
List <double> intensities2 = new List <double>();
foreach (var aok in pepWithSetMods.Fragment(DissociationType.HCD, FragmentationTerminus.Both))
{
mz2.Add(aok.NeutralMass.ToMz(1));
mz2.Add((aok.NeutralMass + Constants.C13MinusC12).ToMz(1));
intensities2.Add(1);
intensities2.Add(1);
}
var MassSpectrum2 = new MzSpectrum(mz2.OrderBy(b => b).ToArray(), intensities2.ToArray(), false);
var scan2 = new MsDataScan(MassSpectrum2, 2, 2, true, Polarity.Positive, 2, new MzLibUtil.MzRange(0, 10000), "df", MZAnalyzerType.Orbitrap, 234734, 1, null, "scan=2", pepWithSetMods.MonoisotopicMass.ToMz(2), 2, 1, pepWithSetMods.MonoisotopicMass.ToMz(2), 2, DissociationType.HCD, 1, pepWithSetMods.MonoisotopicMass.ToMz(2));
scan2.ComputeSelectedPeakIntensity(MassSpectrum1);
scan2.ComputeMonoisotopicPeakIntensity(MassSpectrum1);
ScansHere.Add(scan2);
Scans = ScansHere.ToArray();
}
/// <summary>
/// Tests that a PeptideWithSetModifications object can be parsed correctly from a string, with mod info
/// </summary>
public static void TestReadPeptideFromString()
{
// set up the test
ModificationMotif.TryGetMotif("T", out ModificationMotif target);
Modification carbamidomethylOnC = new Modification(_originalId: "Carbamidomethyl on C", _modificationType: "Common Fixed", _target: target, _chemicalFormula: ChemicalFormula.ParseFormula("C2H3NO"));
string sequence = "HQVC[Common Fixed:Carbamidomethyl on C]TPGGTTIAGLC[Common Fixed:Carbamidomethyl on C]VMEEK";
// parse the peptide from the string
PeptideWithSetModifications peptide = new PeptideWithSetModifications(sequence, new Dictionary <string, Modification> {
{ carbamidomethylOnC.IdWithMotif, carbamidomethylOnC }
});
// test base sequence and full sequence
Assert.That(peptide.BaseSequence == "HQVCTPGGTTIAGLCVMEEK");
Assert.That(peptide.FullSequence == sequence);
// test peptide mass
Assert.That(Math.Round(peptide.MonoisotopicMass, 5) == 2187.01225);
// test mods (correct id, correct number of mods, correct location of mods)
Assert.That(peptide.AllModsOneIsNterminus.First().Value.IdWithMotif == "Carbamidomethyl on C");
Assert.That(peptide.AllModsOneIsNterminus.Count == 2);
Assert.That(new HashSet <int>(peptide.AllModsOneIsNterminus.Keys).SetEquals(new HashSet <int>()
{
5, 16
}));
// calculate fragments. just check that they exist and it doesn't crash
List <Product> theoreticalFragments = new List <Product>();
peptide.Fragment(DissociationType.HCD, FragmentationTerminus.Both, theoreticalFragments);
Assert.That(theoreticalFragments.Count > 0);
}
public TestDataFile(PeptideWithSetModifications pepWithSetMods, string v) : base(2, new SourceFile(null, null, null, null, null))
{
if (v.Equals("quadratic"))
{
// Add three ms1 peaks with charge 2, exact
var MassSpectrum1 = new MzSpectrum(new double[] { pepWithSetMods.MonoisotopicMass.ToMz(2), (pepWithSetMods.MonoisotopicMass + Constants.C13MinusC12).ToMz(2), (pepWithSetMods.MonoisotopicMass + 2 * Constants.C13MinusC12).ToMz(2) }, new double[] { 1, 1, 1 }, false);
List <double> mz2 = new List <double>();
List <double> intensities2 = new List <double>();
foreach (var aok in pepWithSetMods.Fragment(DissociationType.HCD, FragmentationTerminus.Both))
{
var t1 = aok.NeutralMass.ToMz(1);
var c = 0.0000001;
mz2.Add(t1 + c * Math.Pow(t1, 2));
var t2 = (aok.NeutralMass + Constants.C13MinusC12).ToMz(1);
mz2.Add(t2 + c * Math.Pow(t2, 2));
intensities2.Add(1);
intensities2.Add(1);
}
var MassSpectrum2 = new MzSpectrum(mz2.OrderBy(b => b).ToArray(), intensities2.ToArray(), false);
var scan2 = new MsDataScan(MassSpectrum2, 2, 2, true, Polarity.Positive, 2, new MzLibUtil.MzRange(0, 10000), "df", MZAnalyzerType.Orbitrap, 234734, 1, null, "scan=2", pepWithSetMods.MonoisotopicMass.ToMz(2), 2, 1, pepWithSetMods.MonoisotopicMass.ToMz(2), 2, DissociationType.HCD, 1, pepWithSetMods.MonoisotopicMass.ToMz(2));
scan2.ComputeSelectedPeakIntensity(MassSpectrum1);
scan2.ComputeMonoisotopicPeakIntensity(MassSpectrum1);
var ScansHere = new List <MsDataScan> {
new MsDataScan(MassSpectrum1, 1, 1, true, Polarity.Positive, 1, new MzLibUtil.MzRange(0, 10000), "ff", MZAnalyzerType.Unknown, 1000, 1, null, "scan=1"),
scan2
};
Scans = ScansHere.ToArray();
}
}
public static void TestLastPeaks()
{
IDictionary <int, List <Modification> > mods = new Dictionary <int, List <Modification> >();
ModificationMotif.TryGetMotif("M", out ModificationMotif motif);
var prot = new Protein("MMMM", null, null, null, mods);
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 1);
PeptideWithSetModifications thePep = prot.Digest(digestionParams, new List <Modification>(), new List <Modification>()).First();
var massArray = thePep.Fragment(DissociationType.HCD, FragmentationTerminus.Both).Select(p => p.NeutralMass).ToArray();
Array.Sort(massArray);
double[] intensities = new double[] { 1, 1, 1 };
double[] mz = new double[] { 1, 2, massArray[4].ToMz(1) };
MzSpectrum massSpectrum = new MzSpectrum(mz, intensities, false);
MsDataScan scan = new MsDataScan(massSpectrum, 1, 1, true, Polarity.Positive, 1, new MzRange(300, 2000), "", MZAnalyzerType.Unknown, massSpectrum.SumOfAllY, null, null, "scan=1", 0, null, null, 0, null, DissociationType.Unknown, 1, null);
PeptideSpectralMatch[] globalPsms = new PeptideSpectralMatch[1];
Ms2ScanWithSpecificMass[] arrayOfSortedMS2Scans = { new Ms2ScanWithSpecificMass(scan, 0, 1, null, new CommonParameters()) };
CommonParameters CommonParameters = new CommonParameters(
scoreCutoff: 1,
productMassTolerance: new PpmTolerance(5),
digestionParams: new DigestionParams(
maxMissedCleavages: 0,
minPeptideLength: 1,
maxModificationIsoforms: int.MaxValue,
initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain));
ClassicSearchEngine cse = new ClassicSearchEngine(globalPsms, arrayOfSortedMS2Scans, new List <Modification>(), new List <Modification>(), null, new List <Protein> {
prot
}, new OpenSearchMode(), CommonParameters, new List <string>());
cse.Run();
Assert.Less(globalPsms[0].Score, 2);
Assert.Greater(globalPsms[0].Score, 1);
}
public TestDataFile(PeptideWithSetModifications pepWithSetMods, int charge, double intensity, double rt) : base(2, new SourceFile(null, null, null, null, null))
{
var mz1 = new double[] { pepWithSetMods.MonoisotopicMass.ToMz(charge), (pepWithSetMods.MonoisotopicMass + 1.003).ToMz(charge), (pepWithSetMods.MonoisotopicMass + 2.005).ToMz(charge) };
var intensities1 = new double[] { intensity, intensity * 10, intensity / 10 };
var MassSpectrum1 = new MzmlMzSpectrum(mz1, intensities1, false);
var ScansHere = new List <IMzmlScan> {
new MzmlScan(1, MassSpectrum1, 1, true, Polarity.Positive, rt, new MzLibUtil.MzRange(0, 10000), "ff", MZAnalyzerType.Unknown, 1000, 1, "scan=1")
};
List <double> mz2 = new List <double>();
List <double> intensities2 = new List <double>();
foreach (var aok in pepWithSetMods.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.B, ProductType.Y
}))
{
mz2.Add(aok.ToMz(1));
mz2.Add((aok + 1.003).ToMz(1));
intensities2.Add(intensity);
intensities2.Add(intensity);
}
var MassSpectrum2 = new MzmlMzSpectrum(mz2.OrderBy(b => b).ToArray(), intensities2.ToArray(), false);
var scan2 = new MzmlScanWithPrecursor(2, MassSpectrum2, 2, true, Polarity.Positive, rt + 0.01, new MzLibUtil.MzRange(0, 10000), "df", MZAnalyzerType.Orbitrap, 234734, pepWithSetMods.MonoisotopicMass.ToMz(2), 2, 1, pepWithSetMods.MonoisotopicMass.ToMz(2), 2, DissociationType.HCD, 1, pepWithSetMods.MonoisotopicMass.ToMz(2), 1, "scan=2");
scan2.ComputeSelectedPeakIntensity(MassSpectrum1);
scan2.ComputeMonoisotopicPeakIntensity(MassSpectrum1);
ScansHere.Add(scan2);
Scans = ScansHere.ToArray();
}
public void SSRCalc3_100A_Test()
{
SSRCalc3 calc = new SSRCalc3("SSRCalc 3.0 (100A)", SSRCalc3.Column.A100);
for (int i = 0; i < _peptides100A.GetLength(0); i++)
{
var peptide = new PeptideWithSetModifications((string)_peptides100A[i, 0], new Dictionary <string, Modification>());
object obj = _peptides100A[i, 1];
double expected = (double)_peptides100A[i, 1];
double actual = calc.ScoreSequence(peptide);
// Round the returned value to match the values presented
// in the supporting information of the SSRCalc 3 publication.
// First cast to float, since the added precision of the double
// caused the double representation of 12.805 to round to 12.80
// instead of 12.81. When diffed with 12.81 the result was
// 0.005000000000002558.
double actualRound = Math.Round((float)actual, 2);
// Extra conditional added to improve debugging of issues.
if (Math.Abs(expected - actual) > 0.005)
{
Assert.AreEqual(expected, actualRound, "Peptide {0}", peptide);
}
}
}
public TestDataFile(PeptideWithSetModifications pepWithSetMods) : base(2, new SourceFile(@"no nativeID format", "mzML format", null, "SHA-1", @"C:\fake.mzML", null))
{
var mz1 = new double[] { pepWithSetMods.MonoisotopicMass.ToMz(2), (pepWithSetMods.MonoisotopicMass + 1.003).ToMz(2), (pepWithSetMods.MonoisotopicMass + 2.005).ToMz(2) };
var intensities1 = new double[] { 1, 1, 1 };
var MassSpectrum1 = new MzSpectrum(mz1, intensities1, false);
var ScansHere = new List <MsDataScan> {
new MsDataScan(MassSpectrum1, 1, 1, true, Polarity.Positive, 1, new MzLibUtil.MzRange(0, 10000), "ff", MZAnalyzerType.Unknown, 1000, 1, null, "scan=1")
};
List <double> mz2 = new List <double>();
List <double> intensities2 = new List <double>();
foreach (var aok in pepWithSetMods.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.B, ProductType.Y
}))
{
mz2.Add(aok.ToMz(1));
mz2.Add((aok + 1.003).ToMz(1));
intensities2.Add(1);
intensities2.Add(1);
}
var MassSpectrum2 = new MzSpectrum(mz2.OrderBy(b => b).ToArray(), intensities2.ToArray(), false);
var scan2 = new MsDataScan(MassSpectrum2, 2, 2, true, Polarity.Positive, 2, new MzLibUtil.MzRange(0, 10000), "df", MZAnalyzerType.Orbitrap, 234734, 1, null, "scan=2", pepWithSetMods.MonoisotopicMass.ToMz(2), 2, 1, pepWithSetMods.MonoisotopicMass.ToMz(2), 2, DissociationType.HCD, 1, pepWithSetMods.MonoisotopicMass.ToMz(2));
scan2.ComputeSelectedPeakIntensity(MassSpectrum1);
scan2.ComputeMonoisotopicPeakIntensity(MassSpectrum1);
ScansHere.Add(scan2);
Scans = ScansHere.ToArray();
}
public TestDataFile(PeptideWithSetModifications pepWithSetMods, string v) : base(2, new SourceFile(null, null, null, null, null))
{
if (v.Equals("quadratic"))
{
// Add three ms1 peaks with charge 2, exact
var MassSpectrum1 = new MzmlMzSpectrum(new double[] { pepWithSetMods.MonoisotopicMass.ToMz(2), (pepWithSetMods.MonoisotopicMass + 1.003).ToMz(2), (pepWithSetMods.MonoisotopicMass + 2.005).ToMz(2) }, new double[] { 1, 1, 1 }, false);
List <double> mz2 = new List <double>();
List <double> intensities2 = new List <double>();
foreach (var aok in pepWithSetMods.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.B, ProductType.Y
}))
{
var t1 = aok.ToMz(1);
var c = 0.0000001;
mz2.Add(t1 + c * Math.Pow(t1, 2));
var t2 = (aok + 1.003).ToMz(1);
mz2.Add(t2 + c * Math.Pow(t2, 2));
intensities2.Add(1);
intensities2.Add(1);
}
var MassSpectrum2 = new MzmlMzSpectrum(mz2.OrderBy(b => b).ToArray(), intensities2.ToArray(), false);
var scan2 = new MzmlScanWithPrecursor(2, MassSpectrum2, 2, true, Polarity.Positive, 2, new MzLibUtil.MzRange(0, 10000), "df", MZAnalyzerType.Orbitrap, 234734, pepWithSetMods.MonoisotopicMass.ToMz(2), 2, 1, pepWithSetMods.MonoisotopicMass.ToMz(2), 2, DissociationType.HCD, 1, pepWithSetMods.MonoisotopicMass.ToMz(2), 1, "scan=2");
scan2.ComputeSelectedPeakIntensity(MassSpectrum1);
scan2.ComputeMonoisotopicPeakIntensity(MassSpectrum1);
var ScansHere = new List <IMzmlScan> {
new MzmlScan(1, MassSpectrum1, 1, true, Polarity.Positive, 1, new MzLibUtil.MzRange(0, 10000), "ff", MZAnalyzerType.Unknown, 1000, 1, "scan=1"),
scan2
};
Scans = ScansHere.ToArray();
}
}
public TestDataFile(PeptideWithSetModifications pepWithSetMods, int charge, double intensity, double rt) : base(2, new SourceFile(null, null, null, null, null))
{
var mz1 = new double[] { pepWithSetMods.MonoisotopicMass.ToMz(charge), (pepWithSetMods.MonoisotopicMass + 1.003).ToMz(charge), (pepWithSetMods.MonoisotopicMass + 2.005).ToMz(charge) };
var intensities1 = new double[] { intensity, intensity * 10, intensity / 10 };
var MassSpectrum1 = new MzSpectrum(mz1, intensities1, false);
var ScansHere = new List <MsDataScan> {
new MsDataScan(MassSpectrum1, 1, 1, true, Polarity.Positive, rt, new MzLibUtil.MzRange(0, 10000), "ff", MZAnalyzerType.Unknown, 1000, 1, null, "scan=1")
};
List <double> mz2 = new List <double>();
List <double> intensities2 = new List <double>();
foreach (var aok in pepWithSetMods.Fragment(DissociationType.HCD, FragmentationTerminus.Both))
{
mz2.Add(aok.NeutralMass.ToMz(1));
mz2.Add((aok.NeutralMass + 1.003).ToMz(1));
intensities2.Add(intensity);
intensities2.Add(intensity);
}
var MassSpectrum2 = new MzSpectrum(mz2.OrderBy(b => b).ToArray(), intensities2.ToArray(), false);
var scan2 = new MsDataScan(MassSpectrum2, 2, 2, true, Polarity.Positive, rt + 0.01, new MzLibUtil.MzRange(0, 10000), "df", MZAnalyzerType.Orbitrap, 234734, 1, null, "scan=2", pepWithSetMods.MonoisotopicMass.ToMz(2), 2, 1, pepWithSetMods.MonoisotopicMass.ToMz(2), 2, DissociationType.HCD, 1, pepWithSetMods.MonoisotopicMass.ToMz(2));
scan2.ComputeSelectedPeakIntensity(MassSpectrum1);
scan2.ComputeMonoisotopicPeakIntensity(MassSpectrum1);
ScansHere.Add(scan2);
Scans = ScansHere.ToArray();
}
public static PeptideWithSetModifications OGlyGetTheoreticalPeptide(Route theModPositions, PeptideWithSetModifications peptide)
{
Modification[] modifications = new Modification[theModPositions.Mods.Count];
for (int i = 0; i < theModPositions.Mods.Count; i++)
{
modifications[i] = GlycanBox.GlobalOGlycanModifications[theModPositions.Mods[i].Item2];
}
Dictionary <int, Modification> testMods = new Dictionary <int, Modification>();
foreach (var mod in peptide.AllModsOneIsNterminus)
{
testMods.Add(mod.Key, mod.Value);
}
for (int i = 0; i < theModPositions.Mods.Count; i++)
{
testMods.Add(theModPositions.Mods[i].Item1, modifications[i]);
}
var testPeptide = new PeptideWithSetModifications(peptide.Protein, peptide.DigestionParams, peptide.OneBasedStartResidueInProtein,
peptide.OneBasedEndResidueInProtein, peptide.CleavageSpecificityForFdrCategory, peptide.PeptideDescription, peptide.MissedCleavages, testMods, peptide.NumFixedMods);
return(testPeptide);
}
public static IEnumerable <Tuple <int, List <Product> > > XlGetTheoreticalFragments(DissociationType dissociationType, Crosslinker crosslinker,
List <int> possibleCrosslinkerPositions, double otherPeptideMass, PeptideWithSetModifications peptide)
{
List <double> massesToLocalize = new List <double>();
if (crosslinker.Cleavable && crosslinker.CleaveDissociationTypes.Contains(dissociationType))
{
massesToLocalize.Add(crosslinker.CleaveMassShort);
massesToLocalize.Add(crosslinker.CleaveMassLong);
}
else
{
massesToLocalize.Add(crosslinker.TotalMass + otherPeptideMass);
}
var fragments = new List <Product>();
HashSet <double> masses = new HashSet <double>();
foreach (int crosslinkerPosition in possibleCrosslinkerPositions)
{
List <Product> theoreticalProducts = new List <Product>(); //need a new one each time to pass as a reference, don't clear
masses.Clear();
foreach (double massToLocalize in massesToLocalize)
{
Dictionary <int, Modification> testMods = new Dictionary <int, Modification> {
{ crosslinkerPosition + 1, new Modification(_monoisotopicMass: massToLocalize) }
};
foreach (var mod in peptide.AllModsOneIsNterminus)
{
testMods.Add(mod.Key, mod.Value);
}
var testPeptide = new PeptideWithSetModifications(peptide.Protein, peptide.DigestionParams, peptide.OneBasedStartResidueInProtein,
peptide.OneBasedEndResidueInProtein, peptide.CleavageSpecificityForFdrCategory, peptide.PeptideDescription, peptide.MissedCleavages, testMods, peptide.NumFixedMods);
testPeptide.Fragment(dissociationType, FragmentationTerminus.Both, fragments);
// add fragmentation ions for this crosslinker position guess
foreach (var fragment in fragments)
{
if (!masses.Contains(fragment.NeutralMass))
{
theoreticalProducts.Add(fragment);
masses.Add(fragment.NeutralMass);
}
}
// add signature ions
if (crosslinker.Cleavable)
{
theoreticalProducts.Add(new Product(ProductType.M, FragmentationTerminus.None, peptide.MonoisotopicMass + massToLocalize,
peptide.Length, peptide.Length, 0));
}
}
yield return(new Tuple <int, List <Product> >(crosslinkerPosition, theoreticalProducts));
}
}
//Motif should be writen with required form
public static List <int> GetPossibleModSites(PeptideWithSetModifications peptide, string[] motifs)
{
List <int> possibleModSites = new List <int>();
List <Modification> modifications = new List <Modification>();
foreach (var mtf in motifs)
{
if (ModificationMotif.TryGetMotif(mtf, out ModificationMotif aMotif))
{
Modification modWithMotif = new Modification(_target: aMotif, _locationRestriction: "Anywhere.");
modifications.Add(modWithMotif);
}
}
foreach (var modWithMotif in modifications)
{
for (int r = 0; r < peptide.Length; r++)
{
if (peptide.AllModsOneIsNterminus.Keys.Contains(r + 2))
{
continue;
}
//FullSequence is used here to avoid duplicated modification on same sites?
if (ModificationLocalization.ModFits(modWithMotif, peptide.BaseSequence, r + 1, peptide.Length, r + 1))
{
possibleModSites.Add(r + 2);
}
}
}
return(possibleModSites);
}
private static double GetCifuentesMobility(PeptideWithSetModifications pwsm)
{
int charge = 1 + pwsm.BaseSequence.Count(f => f == 'K') + pwsm.BaseSequence.Count(f => f == 'R') + pwsm.BaseSequence.Count(f => f == 'H') - CountModificationsThatShiftMobility(pwsm.AllModsOneIsNterminus.Values.AsEnumerable());// the 1 + is for N-terminal
double mobility = (Math.Log(1 + 0.35 * (double)charge)) / Math.Pow(pwsm.MonoisotopicMass, 0.411);
return(mobility);
}
public static void TestLocalization()
{
var protease = new Protease("Custom Protease", new List <string> {
"K"
}, new List <string>(), TerminusType.C, CleavageSpecificity.Full, null, null, null);
Protein parentProteinForMatch = new Protein("MEK", null);
DigestionParams digestionParams = new DigestionParams
{
MinPeptideLength = 1,
};
ModificationMotif.TryGetMotif("E", out ModificationMotif motif);
List <ModificationWithMass> variableModifications = new List <ModificationWithMass> {
new ModificationWithMass("21", null, motif, TerminusLocalization.Any, 21.981943)
};
List <PeptideWithSetModifications> allPeptidesWithSetModifications = parentProteinForMatch.Digest(digestionParams, new List <ModificationWithMass>(), variableModifications).ToList();
Assert.AreEqual(4, allPeptidesWithSetModifications.Count());
PeptideWithSetModifications ps = allPeptidesWithSetModifications.First();
List <ProductType> lp = new List <ProductType> {
ProductType.BnoB1ions, ProductType.Y
};
PeptideWithSetModifications pepWithSetModsForSpectrum = allPeptidesWithSetModifications[1];
IMsDataFile <IMsDataScan <IMzSpectrum <IMzPeak> > > myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications> {
pepWithSetModsForSpectrum
});
Tolerance fragmentTolerance = new AbsoluteTolerance(0.01);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(myMsDataFile.Last() as IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> >, pepWithSetModsForSpectrum.MonoisotopicMass.ToMz(1), 1, null);
PeptideSpectralMatch newPsm = new PeptideSpectralMatch(ps.CompactPeptide(TerminusType.None), 0, 0, 2, scan);
Dictionary <ModificationWithMass, ushort> modsDictionary = new Dictionary <ModificationWithMass, ushort>();
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > matching = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >
{
{ ps.CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> {
ps
} }
};
newPsm.MatchToProteinLinkedPeptides(matching);
LocalizationEngine f = new LocalizationEngine(new List <PeptideSpectralMatch> {
newPsm
}, lp, myMsDataFile, fragmentTolerance, new List <string>(), false);
f.Run();
// Was single peak!!!
Assert.AreEqual(0, newPsm.MatchedIonDictOnlyMatches[ProductType.BnoB1ions].Count(b => b > 0));
Assert.AreEqual(1, newPsm.MatchedIonDictOnlyMatches[ProductType.Y].Count(b => b > 0));
// If localizing, three match!!!
Assert.IsTrue(newPsm.LocalizedScores[1] > 3 && newPsm.LocalizedScores[1] < 4);
}
public CrosslinkSpectralMatch(PeptideWithSetModifications theBestPeptide, int notch, double score, int scanIndex, Ms2ScanWithSpecificMass scan, CommonParameters commonParameters, List <MatchedFragmentIon> matchedFragmentIons)
: base(theBestPeptide, notch, score, scanIndex, scan, commonParameters, matchedFragmentIons)
{
//The XLTotalScore is set here because some CSMs are not crosslinks and we need this score to be non-zero.
XLTotalScore = score;
_BestMatchingPeptides.Clear();
_BestMatchingPeptides.Add((0, theBestPeptide));
}
public static void ReplaceBadStdevTwo()
{
//here we are adding a really hydrophobic psm at the same time as a regular peptide so that there is a big difference in their computed hydrophobicities. The stdev of these hydrophobicities is out of whach the the collective and so it needs to get replaced by the global average
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var origDataFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\TaGe_SA_HeLa_04_subset_longestSeq.mzML");
MyFileManager myFileManager = new MyFileManager(true);
CommonParameters CommonParameters = new CommonParameters(digestionParams: new DigestionParams());
var myMsDataFile = myFileManager.LoadFile(origDataFile, CommonParameters);
var searchModes = new SinglePpmAroundZeroSearchMode(5);
List <Protein> proteinList = ProteinDbLoader.LoadProteinFasta(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\hela_snip_for_unitTest.fasta"), true, DecoyType.Reverse, false, ProteinDbLoader.UniprotAccessionRegex, ProteinDbLoader.UniprotFullNameRegex, ProteinDbLoader.UniprotFullNameRegex, ProteinDbLoader.UniprotGeneNameRegex,
ProteinDbLoader.UniprotOrganismRegex, out var dbErrors, -1);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, @"TestData\TaGe_SA_HeLa_04_subset_longestSeq.mzML", CommonParameters).OrderBy(b => b.PrecursorMass).ToArray();
//adding a new scan that creates a psm at an isolated retention time. This will ultimately cause PEP to replace its retention time standard deviation "Z-score" with the global average.
Ms2ScanWithSpecificMass topMs2Scan = listOfSortedms2Scans[395];
int newOneBasedScanNumber = 1000;
MzRange range = new MzRange(topMs2Scan.TheScan.MassSpectrum.XArray.Min(), topMs2Scan.TheScan.MassSpectrum.XArray.Max());
MzSpectrum mzs = new MzSpectrum(topMs2Scan.TheScan.MassSpectrum.XArray, topMs2Scan.TheScan.MassSpectrum.YArray, true);
double newRetentionTime = topMs2Scan.TheScan.RetentionTime - 25;
MsDataScan msd = new MsDataScan(mzs, newOneBasedScanNumber, 2, topMs2Scan.TheScan.IsCentroid, Polarity.Positive, newRetentionTime, range, "", MZAnalyzerType.Orbitrap, topMs2Scan.TheScan.TotalIonCurrent, topMs2Scan.TheScan.InjectionTime, topMs2Scan.TheScan.NoiseData, "", topMs2Scan.TheScan.SelectedIonMZ, topMs2Scan.TheScan.SelectedIonChargeStateGuess, topMs2Scan.TheScan.SelectedIonIntensity, topMs2Scan.TheScan.IsolationMz, topMs2Scan.TheScan.IsolationWidth, DissociationType.HCD, topMs2Scan.TheScan.OneBasedPrecursorScanNumber, topMs2Scan.TheScan.SelectedIonMonoisotopicGuessMz);
Ms2ScanWithSpecificMass mwsm = new Ms2ScanWithSpecificMass(msd, topMs2Scan.PrecursorMonoisotopicPeakMz, topMs2Scan.PrecursorCharge, topMs2Scan.FullFilePath, new CommonParameters(), topMs2Scan.ExperimentalFragments);
Ms2ScanWithSpecificMass[] extendedArray = new Ms2ScanWithSpecificMass[listOfSortedms2Scans.Length + 1];
for (int i = 0; i < listOfSortedms2Scans.Length; i++)
{
extendedArray[i] = listOfSortedms2Scans[i];
}
extendedArray[listOfSortedms2Scans.Length] = mwsm;
extendedArray = extendedArray.OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[extendedArray.Length];
new ClassicSearchEngine(allPsmsArray, extendedArray, variableModifications, fixedModifications, null, null, null, proteinList, searchModes, CommonParameters, new List <string>()).Run();
List <PeptideSpectralMatch> nonNullPsms = allPsmsArray.Where(p => p != null).ToList();
nonNullPsms = nonNullPsms.OrderByDescending(p => p.Score).ToList();
List <PeptideSpectralMatch> psmBloated = new List <PeptideSpectralMatch>();
psmBloated.AddRange(nonNullPsms);
int arrayMax = nonNullPsms.Count;
psmBloated.AddRange(nonNullPsms.GetRange(2, arrayMax - 2));
psmBloated.AddRange(nonNullPsms.GetRange(2, arrayMax - 2));
PeptideSpectralMatch pp = psmBloated.Where(p => p.ScanRetentionTime < (newRetentionTime + 1)).First();
PeptideWithSetModifications newPwsmTwo = new PeptideWithSetModifications(new Protein("WAGVLPWFPWAAVVWGFWF", "ACCESSION", "ORGANISM"), new DigestionParams(), 1, 2, CleavageSpecificity.Full, "", 0, new Dictionary <int, Modification>(), 0);
PeptideSpectralMatch newPsmTwo = new PeptideSpectralMatch(newPwsmTwo, pp.BestMatchingPeptides.First().Notch, pp.Score, pp.ScanIndex, mwsm, new DigestionParams(), pp.MatchedFragmentIons);
psmBloated.Add(newPsmTwo);
FdrAnalysisResults fdrResultsClassicDelta = (FdrAnalysisResults)(new FdrAnalysisEngine(psmBloated.Where(p => p != null).ToList(), 1, CommonParameters, new List <string>()).Run());
}
public static void TestUniProtGptmdConflict()
{
// this unit test checks to make sure GPTMD does not annotate mods at residues on
// proteins where the equivalent uniprot mod already exists
Modification uniProtPhospho = GlobalVariables.AllModsKnown.First(p => p.ModificationType == "UniProt" && p.IdWithMotif.Contains("Phosphoserine"));
Modification mmPhospho = GlobalVariables.AllModsKnown.First(p => p.ModificationType == "Common Biological" && p.IdWithMotif.Contains("Phosphorylation on S"));
Protein protein = new Protein("PEPTIDESK", "test",
oneBasedModifications: new Dictionary <int, List <Modification> >()
{
{ 8, new List <Modification> {
uniProtPhospho
} }
});
PeptideWithSetModifications pep = protein.Digest(new DigestionParams(), new List <Modification>(), new List <Modification>()).First(p => p.AllModsOneIsNterminus.Count == 0);
// mod should not fit anywhere on the protein
for (int i = 0; i < pep.Length; i++)
{
bool modFits = GptmdEngine.ModFits(mmPhospho, protein, i + 1, pep.Length, pep.OneBasedStartResidueInProtein + i);
Assert.That(!modFits);
}
// the following code is just a control to make sure the phosphorylation actually does fit
// at the given residue if the UniProt phosphorylation is not already present
var someOtherSMod = GlobalVariables.AllModsKnown.Where(p => p.ModificationType == "Common Biological" && p.IdWithMotif.Contains("HexNAc on S")).First();
protein = new Protein("PEPTIDESK", "test",
oneBasedModifications: new Dictionary <int, List <Modification> >()
{
{ 8, new List <Modification> {
someOtherSMod
} }
});
pep = protein.Digest(new DigestionParams(), new List <Modification>(), new List <Modification>()).First(p => p.AllModsOneIsNterminus.Count == 0);
// mod should fit at position 8
for (int i = 0; i < pep.Length; i++)
{
bool modFits = GptmdEngine.ModFits(mmPhospho, protein, i + 1, pep.Length, pep.OneBasedStartResidueInProtein + i);
if (i + 1 == 8)
{
Assert.That(modFits);
}
else
{
Assert.That(!modFits);
}
}
}
protected override MetaMorpheusEngineResults RunSpecific()
{
TerminusType terminusType = ProductTypeMethod.IdentifyTerminusType(lp);
foreach (var ok in allResultingIdentifications)
{
ok.MatchedIonDictOnlyMatches = new Dictionary <ProductType, double[]>();
ok.ProductMassErrorDa = new Dictionary <ProductType, double[]>();
ok.ProductMassErrorPpm = new Dictionary <ProductType, double[]>();
var theScan = myMsDataFile.GetOneBasedScan(ok.ScanNumber);
double thePrecursorMass = ok.ScanPrecursorMass;
foreach (var huh in lp)
{
var ionMasses = ok.CompactPeptides.First().Key.ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
huh
});
Array.Sort(ionMasses);
List <double> matchedIonMassesList = new List <double>();
List <double> productMassErrorDaList = new List <double>();
List <double> productMassErrorPpmList = new List <double>();
MatchIons(theScan, fragmentTolerance, ionMasses, matchedIonMassesList, productMassErrorDaList, productMassErrorPpmList, thePrecursorMass, dissociationTypes, addCompIons);
double[] matchedIonMassesOnlyMatches = matchedIonMassesList.ToArray();
ok.MatchedIonDictOnlyMatches.Add(huh, matchedIonMassesOnlyMatches);
ok.ProductMassErrorDa.Add(huh, productMassErrorDaList.ToArray());
ok.ProductMassErrorPpm.Add(huh, productMassErrorPpmList.ToArray());
}
}
foreach (var ok in allResultingIdentifications.Where(b => b.NumDifferentCompactPeptides == 1))
{
var theScan = myMsDataFile.GetOneBasedScan(ok.ScanNumber);
double thePrecursorMass = ok.ScanPrecursorMass;
if (ok.FullSequence == null)
{
continue;
}
var representative = ok.CompactPeptides.First().Value.Item2.First();
var localizedScores = new List <double>();
for (int indexToLocalize = 0; indexToLocalize < representative.Length; indexToLocalize++)
{
PeptideWithSetModifications localizedPeptide = representative.Localize(indexToLocalize, ok.ScanPrecursorMass - representative.MonoisotopicMass);
var gg = localizedPeptide.CompactPeptide(terminusType).ProductMassesMightHaveDuplicatesAndNaNs(lp);
Array.Sort(gg);
var score = CalculatePeptideScore(theScan, fragmentTolerance, gg, thePrecursorMass, dissociationTypes, addCompIons, 0);
localizedScores.Add(score);
}
ok.LocalizedScores = localizedScores;
}
return(new LocalizationEngineResults(this));
}
public TestDataFile(PeptideWithSetModifications pwsm, List <double> labelMassDifferences, bool includeMassDifferenceInPrecursor = false)
: base(2, new SourceFile(@"no nativeID format", "mzML format", null, "SHA-1", @"C:\fake.mzML", null))
{
List <MsDataScan> ScansHere = new List <MsDataScan>();
double lightMass = pwsm.MonoisotopicMass;
for (int i = 0; i < labelMassDifferences.Count; i++)
{
labelMassDifferences[i] += lightMass;
}
labelMassDifferences.Insert(0, lightMass);
List <double> mz1 = new List <double>();
List <double> intensities1 = new List <double>();
for (int z = 3; z >= 2; z--)
{
for (int i = 0; i < labelMassDifferences.Count; i++)
{
double mass = labelMassDifferences[i];
for (int isotope = 0; isotope < 3; isotope++)
{
mz1.Add((mass + isotope * Constants.C13MinusC12).ToMz(z));
intensities1.Add(Math.Pow(0.5, i) * (Math.Pow(0.5, isotope) * 1000000)); //makes each label half the intensity of the previous
}
}
}
var MassSpectrum1 = new MzSpectrum(mz1.ToArray(), intensities1.ToArray(), false);
ScansHere.Add(new MsDataScan(MassSpectrum1, 1, 1, true, Polarity.Positive, 0, new MzLibUtil.MzRange(0, 10000), "gg", MZAnalyzerType.Orbitrap, 1000, 1, null, "scan=1"));
//only make the light ms2, it should find the heavy ms1 from that
List <double> mz2 = new List <double>();
List <double> intensities2 = new List <double>();
foreach (var aok in pwsm.Fragment(DissociationType.HCD, FragmentationTerminus.Both))
{
mz2.Add(aok.NeutralMass.ToMz(1));
mz2.Add((aok.NeutralMass + Constants.C13MinusC12).ToMz(1));
intensities2.Add(1);
intensities2.Add(1);
}
if (includeMassDifferenceInPrecursor)
{
lightMass = labelMassDifferences[1];
}
var MassSpectrum2 = new MzSpectrum(mz2.OrderBy(b => b).ToArray(), intensities2.ToArray(), false);
ScansHere.Add(new MsDataScan(MassSpectrum2, 2, 2, true, Polarity.Positive, 1, new MzLibUtil.MzRange(0, 10000), "gg", MZAnalyzerType.Orbitrap, 234734, 1, null, "scan=2", lightMass.ToMz(2), 2, 1, lightMass.ToMz(2), 2, DissociationType.HCD, 1, lightMass.ToMz(2)));
Scans = ScansHere.ToArray();
}
public static void TestXicExtraction()
{
string dataFilePath = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", "SmallCalibratibleYeast.mzml");
var data = Mzml.LoadAllStaticData(dataFilePath);
var peptide = new PeptideWithSetModifications("KAPAGGAADAAAK", new Dictionary <string, Modification>());
var xic = data.ExtractIonChromatogram(peptide.MonoisotopicMass, 2, new PpmTolerance(10), 24.806);
Assert.That(xic.Data.Count(p => p.Y > 0) == 4);
}
public static void TestLocalization()
{
Protein parentProteinForMatch = new Protein("MEK", null);
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 1);
ModificationMotif.TryGetMotif("E", out ModificationMotif motif);
List <ModificationWithMass> variableModifications = new List <ModificationWithMass> {
new ModificationWithMass("21", null, motif, TerminusLocalization.Any, 21.981943)
};
List <PeptideWithSetModifications> allPeptidesWithSetModifications = parentProteinForMatch.Digest(digestionParams, new List <ModificationWithMass>(), variableModifications).ToList();
Assert.AreEqual(4, allPeptidesWithSetModifications.Count());
PeptideWithSetModifications ps = allPeptidesWithSetModifications.First();
List <ProductType> lp = new List <ProductType> {
ProductType.BnoB1ions, ProductType.Y
};
PeptideWithSetModifications pepWithSetModsForSpectrum = allPeptidesWithSetModifications[1];
MsDataFile myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications> {
pepWithSetModsForSpectrum
});
Tolerance fragmentTolerance = new AbsoluteTolerance(0.01);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(myMsDataFile.GetAllScansList().Last(), pepWithSetModsForSpectrum.MonoisotopicMass.ToMz(1), 1, null);
PeptideSpectralMatch newPsm = new PeptideSpectralMatch(ps.CompactPeptide(TerminusType.None), 0, 0, 2, scan, digestionParams);
Dictionary <ModificationWithMass, ushort> modsDictionary = new Dictionary <ModificationWithMass, ushort>();
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > matching = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >
{
{ ps.CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> {
ps
} }
};
newPsm.MatchToProteinLinkedPeptides(matching);
CommonParameters commonParameters = new CommonParameters(productMassTolerance: fragmentTolerance);
LocalizationEngine f = new LocalizationEngine(new List <PeptideSpectralMatch> {
newPsm
}, lp, myMsDataFile, commonParameters, new List <string>());
f.Run();
// Was single peak!!!
Assert.AreEqual(0, newPsm.MatchedIonMassToChargeRatioDict[ProductType.BnoB1ions].Count(b => b > 0));
Assert.AreEqual(1, newPsm.MatchedIonMassToChargeRatioDict[ProductType.Y].Count(b => b > 0));
Assert.AreEqual(0, newPsm.MatchedIonIntensitiesDict[ProductType.BnoB1ions].Count(b => b > 0));
Assert.AreEqual(1, newPsm.MatchedIonIntensitiesDict[ProductType.Y].Count(b => b > 0));
// If localizing, three match!!!
Assert.IsTrue(newPsm.LocalizedScores[1] > 3 && newPsm.LocalizedScores[1] < 4);
}
public static List <Product> GetGlycanYIons(PeptideWithSetModifications peptide, Glycan glycan)
{
double possiblePeptideMass = peptide.MonoisotopicMass;
List <Product> YIons = new List <Product>();
YIons.Add(new Product(ProductType.M, FragmentationTerminus.Both, possiblePeptideMass + (double)glycan.Mass / 1E5, 0, 0, (double)glycan.Mass / 1E5));
foreach (var ion in glycan.Ions)
{
Product product = new Product(ProductType.M, FragmentationTerminus.Both, possiblePeptideMass + (double)glycan.Mass / 1E5, 0, 0, (double)ion.LossIonMass / 1E5);
YIons.Add(product);
}
return(YIons);
}
public static void RemoveAmbiguousPeptides()
{
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var origDataFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\TaGe_SA_HeLa_04_subset_longestSeq.mzML");
MyFileManager myFileManager = new MyFileManager(true);
CommonParameters CommonParameters = new CommonParameters(digestionParams: new DigestionParams());
var myMsDataFile = myFileManager.LoadFile(origDataFile, CommonParameters);
var searchModes = new SinglePpmAroundZeroSearchMode(5);
List <Protein> proteinList = ProteinDbLoader.LoadProteinFasta(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\hela_snip_for_unitTest.fasta"), true, DecoyType.Reverse, false, ProteinDbLoader.UniprotAccessionRegex, ProteinDbLoader.UniprotFullNameRegex, ProteinDbLoader.UniprotFullNameRegex, ProteinDbLoader.UniprotGeneNameRegex,
ProteinDbLoader.UniprotOrganismRegex, out var dbErrors, -1);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, @"TestData\TaGe_SA_HeLa_04_subset_longestSeq.mzML", CommonParameters).OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null, proteinList, searchModes, CommonParameters, new List <string>()).Run();
var nonNullPsms = allPsmsArray.Where(p => p != null).ToList();
nonNullPsms.OrderByDescending(p => p.Score);
var maxScore = nonNullPsms.Select(n => n.Score).Max();
PeptideSpectralMatch maxScorePsm = nonNullPsms.Where(n => n.Score == maxScore).First();
Protein newProteinToRemove = new Protein("RREMVE", "BUBBA", isDecoy: false);
PeptideWithSetModifications pwsmToRemove = new PeptideWithSetModifications(newProteinToRemove, new DigestionParams(), 1, 6, CleavageSpecificity.Full, "peptideDescription", 2, new Dictionary <int, Modification>(), 1, "RREMVE");
maxScorePsm.AddOrReplace(pwsmToRemove, maxScore, 1, true, maxScorePsm.MatchedFragmentIons, maxScore);
maxScorePsm.ResolveAllAmbiguities();
List <PeptideSpectralMatch> psmBloated = new List <PeptideSpectralMatch>();
psmBloated.AddRange(nonNullPsms);
psmBloated.AddRange(nonNullPsms.GetRange(0, nonNullPsms.Count - 2));
foreach (PeptideSpectralMatch psm in nonNullPsms.GetRange(0, nonNullPsms.Count - 2))
{
Protein newDecoyProtein = new Protein(psm.BestMatchingPeptides.First().Peptide.BaseSequence + "K", "DECOY_" + psm.BestMatchingPeptides.First().Peptide.Protein.Accession, isDecoy: true);
PeptideWithSetModifications pwsmDecoy = new PeptideWithSetModifications(newDecoyProtein, new DigestionParams(), 1, psm.BestMatchingPeptides.First().Peptide.BaseSequence.Length + 1, CleavageSpecificity.Full, "peptideDescription", 2, new Dictionary <int, Modification>(), 1, psm.BestMatchingPeptides.First().Peptide.BaseSequence + "K");
PeptideSpectralMatch decoyPsm = new PeptideSpectralMatch(pwsmDecoy, 1, psm.Score, psm.ScanIndex, listOfSortedms2Scans[psm.ScanIndex], new DigestionParams(), psm.MatchedFragmentIons);
decoyPsm.ResolveAllAmbiguities();
psmBloated.Add(decoyPsm);
}
PeptideSpectralMatch oldBloatedMaxScorePsm = psmBloated.Where(n => n.Score == maxScore).First();
int countOfBestPeptidesBloatedMax = oldBloatedMaxScorePsm.BestMatchingPeptides.Count();
FdrAnalysisResults fdrResultsClassicDelta = (FdrAnalysisResults)(new FdrAnalysisEngine(psmBloated.Where(p => p != null).ToList(), 1, CommonParameters, new List <string>()).Run());
PeptideSpectralMatch newMaxScorePsm = psmBloated.Where(n => n.Score == maxScore).First();
Assert.AreEqual(countOfBestPeptidesBloatedMax - 1, newMaxScorePsm.BestMatchingPeptides.Count());
}
public static void TestSerializationPeptideFromProtein()
{
// purpose of this test is to serialize/deserialize a PeptideWithSetModifications and make sure the deserialized peptide
// has the same properties as before it was serialized. This peptide is unmodified and generated from digesting a protein
Protein protein = new Protein("PEPTIDE", "Accession1", name: "MyProtein");
PeptideWithSetModifications peptide = protein.Digest(new DigestionParams(), new List <Modification>(), new List <Modification>()).First();
PeptideWithSetModifications deserializedPeptide = null;
string dir = System.IO.Path.Combine(TestContext.CurrentContext.TestDirectory, "TestSerializationPeptideFromProtein");
System.IO.Directory.CreateDirectory(dir);
string path = System.IO.Path.Combine(dir, "myPeptideIndex.ind");
var messageTypes = typeof(PeptideWithSetModifications);
var ser = new NetSerializer.Serializer(new List <Type> {
messageTypes
});
using (var file = System.IO.File.Create(path))
{
ser.Serialize(file, peptide);
}
using (var file = System.IO.File.OpenRead(path))
{
deserializedPeptide = (PeptideWithSetModifications)ser.Deserialize(file);
}
deserializedPeptide.SetNonSerializedPeptideInfo(new Dictionary <string, Modification>(), new Dictionary <string, Protein> {
{ protein.Accession, protein }
}, peptide.DigestionParams);
Assert.That(peptide.DigestionParams.Equals(deserializedPeptide.DigestionParams));
Assert.That(peptide.Equals(deserializedPeptide));
Assert.That(deserializedPeptide.Protein.Name == peptide.Protein.Name);
Assert.That(deserializedPeptide.MonoisotopicMass == peptide.MonoisotopicMass);
Assert.That(deserializedPeptide.SequenceWithChemicalFormulas == peptide.SequenceWithChemicalFormulas);
var products = new List <Product>();
deserializedPeptide.Fragment(DissociationType.HCD, FragmentationTerminus.Both, products);
List <double> deserializedPeptideFragments = products.Select(v => v.NeutralMass).ToList();
peptide.Fragment(DissociationType.HCD, FragmentationTerminus.Both, products);
List <double> peptideFragments = products.Select(v => v.NeutralMass).ToList();
Assert.That(deserializedPeptideFragments.SequenceEqual(peptideFragments));
}
