Пример #1
0
        public static void DifferentAnalyzersTest()
        {
            IMzmlScan[] scans = new IMzmlScan[2];

            double[]       intensities1 = new double[] { 1 };
            double[]       mz1          = new double[] { 50 };
            MzmlMzSpectrum massSpec1    = new MzmlMzSpectrum(mz1, intensities1, false);

            scans[0] = new MzmlScan(1, massSpec1, 1, true, Polarity.Positive, 1, new MzRange(1, 100), "f", MZAnalyzerType.Orbitrap, massSpec1.SumOfAllY, null, "1");

            double[]       intensities2 = new double[] { 1 };
            double[]       mz2          = new double[] { 30 };
            MzmlMzSpectrum massSpec2    = new MzmlMzSpectrum(mz2, intensities2, false);

            scans[1] = new MzmlScanWithPrecursor(2, massSpec2, 2, true, Polarity.Positive, 2, new MzRange(1, 100), "f", MZAnalyzerType.IonTrap3D, massSpec2.SumOfAllY,
                                                 50, null, null, 50, 1, DissociationType.CID, 1, null, null, "2");

            FakeMsDataFile f = new FakeMsDataFile(scans);

            MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(f, Path.Combine(TestContext.CurrentContext.TestDirectory, "asdfefsf.mzML"), false);

            Mzml ok = Mzml.LoadAllStaticData(Path.Combine(TestContext.CurrentContext.TestDirectory, "asdfefsf.mzML"));

            Assert.AreEqual(MZAnalyzerType.Orbitrap, ok.First().MzAnalyzer);
            Assert.AreEqual(MZAnalyzerType.IonTrap3D, ok.Last().MzAnalyzer);
        }
Пример #2
0
        public void WriteMzmlTest()
        {
            var peptide = new Peptide("GPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILR");
            ChemicalFormulaModification carbamidomethylationOfCMod = new ChemicalFormulaModification("H3C2NO", "carbamidomethylation of C", ModificationSites.C);


            peptide.AddModification(carbamidomethylationOfCMod);

            DefaultMzSpectrum MS1 = createSpectrum(peptide.GetChemicalFormula(), 300, 2000, 1);
            DefaultMzSpectrum MS2 = createMS2spectrum(peptide.Fragment(FragmentTypes.b | FragmentTypes.y, true), 100, 1500);

            MsDataScan <IMzSpectrum <MzPeak> >[] Scans = new MsDataScan <IMzSpectrum <MzPeak> > [2];
            Scans[0] = new MsDataScan <IMzSpectrum <MzPeak> >(1, MS1.newSpectrumApplyFunctionToX(b => b + 0.000001 * b + 0.000001), "spectrum 1", 1, false, Polarity.Positive, 1.0, new MzRange(300, 2000), "FTMS first spectrum", MZAnalyzerType.Unknown, 1, MS1.SumOfAllY);

            Scans[1] = new MsDataScan <IMzSpectrum <MzPeak> >(2, MS2.newSpectrumApplyFunctionToX(b => b + 0.00001 * b + 0.00001), "spectrum 2", 2, false, Polarity.Positive, 2.0, new MzRange(100, 1500), "FTMS second spectrum", MZAnalyzerType.Unknown, 1, MS2.SumOfAllY, "spectrum 1", 1134.26091302033, 3, 0.141146966879759, 1134.3, 1, DissociationType.Unknown, 1, 0.141146966879759, 1134.26091302033);

            var myMsDataFile = new FakeMsDataFile(@"myFakeFile.mzML", Scans);

            MzmlMethods.CreateAndWriteMyIndexedMZmlwithCalibratedSpectra(myMsDataFile, Path.Combine(Path.GetDirectoryName(myMsDataFile.FilePath), Path.GetFileNameWithoutExtension(myMsDataFile.FilePath)) + ".mzML");

            Mzml okay = new Mzml(@"myFakeFile.mzML");

            okay.Open();
            okay.GetScan(2);

            Assert.AreEqual(1, okay.GetSpectrumNumber(1));
            Assert.AreEqual(2, okay.GetSpectrumNumber(2));
        }
Пример #3
0
        public void DataFileTest()
        {
            MsDataScan theSpectrum = new MsDataScan(_mzSpectrumA, 1, 1, true, Polarity.Positive, 1, new MzRange(300, 1000), "fake scan filter", MZAnalyzerType.Unknown, _mzSpectrumA.SumOfAllY, 1, null, "scan=1");

            MsDataScan[] theList = new MsDataScan[1];

            theList[0] = theSpectrum;

            FakeMsDataFile thefile = new FakeMsDataFile(theList);

            var theOneBasedScan = thefile.GetOneBasedScan(1);

            Assert.AreEqual("Scan #1", theOneBasedScan.ToString());

            Assert.AreEqual(15, theOneBasedScan.MassSpectrum.Size);
            Assert.AreEqual(15, theOneBasedScan.MassSpectrum.Size);

            Assert.AreEqual(1, thefile.NumSpectra);
            Assert.AreEqual(1, thefile.NumSpectra);

            Assert.IsTrue(thefile.GetOneBasedScan(1).IsCentroid);

            foreach (var ok in thefile)
            {
                Assert.AreEqual(300, ok.ScanWindowRange.Minimum, 1e-9);
                Assert.AreEqual(1000, ok.ScanWindowRange.Maximum, 1e-9);
            }

            int ok1 = 0;

            foreach (var i in thefile.GetMsScansInTimeRange(0, 2))
            {
                ok1 += 1;
            }

            Assert.AreEqual(1, ok1);

            int ok2 = 0;

            foreach (var i in thefile.GetMsScansInTimeRange(2, 4))
            {
                ok2 += 1;
            }

            Assert.AreEqual(0, ok2);

            int ok3 = 0;

            foreach (var i in thefile.GetMsScansInTimeRange(-4, -2))
            {
                ok3 += 1;
            }

            Assert.AreEqual(0, ok3);
        }
Пример #4
0
        public static void WriteEmptyScan()
        {
            double[]       intensities1 = new double[] { };
            double[]       mz1          = new double[] { };
            MzmlMzSpectrum massSpec1    = new MzmlMzSpectrum(mz1, intensities1, false);

            IMzmlScan[] scans = new IMzmlScan[] {
                new MzmlScan(1, massSpec1, 1, true, Polarity.Positive, 1, new MzRange(1, 100), "f", MZAnalyzerType.Orbitrap, massSpec1.SumOfAllY, null, "1")
            };
            FakeMsDataFile f = new FakeMsDataFile(scans);

            MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(f, Path.Combine(TestContext.CurrentContext.TestDirectory, "mzmlWithEmptyScan.mzML"), false);

            Mzml ok = Mzml.LoadAllStaticData(Path.Combine(TestContext.CurrentContext.TestDirectory, "mzmlWithEmptyScan.mzML"));

            MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(ok, Path.Combine(TestContext.CurrentContext.TestDirectory, "mzmlWithEmptyScan2.mzML"), false);
        }
Пример #5
0
        public void WriteMzmlTest()
        {
            var peptide = new Peptide("GPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILR");
            OldSchoolChemicalFormulaModification carbamidomethylationOfCMod = new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("H3C2NO"), "carbamidomethylation of C", ModificationSites.C);

            peptide.AddModification(carbamidomethylationOfCMod);

            MzmlMzSpectrum MS1 = CreateSpectrum(peptide.GetChemicalFormula(), 300, 2000, 1);

            MzmlMzSpectrum MS2 = CreateMS2spectrum(peptide.Fragment(FragmentTypes.b | FragmentTypes.y, true), 100, 1500);

            IMzmlScan[] Scans = new IMzmlScan[2];

            Scans[0] = new MzmlScan(1, MS1, 1, true, Polarity.Positive, 1.0, new MzRange(300, 2000), " first spectrum", MZAnalyzerType.Unknown, MS1.SumOfAllY, 1, "scan=1");

            Scans[1] = new MzmlScanWithPrecursor(2, MS2, 2, true, Polarity.Positive, 2.0, new MzRange(100, 1500), " second spectrum", MZAnalyzerType.Unknown, MS2.SumOfAllY, 1134.26091302033, 3, 0.141146966879759, 1134.3, 1, DissociationType.Unknown, 1, 1134.26091302033, 1, "scan=2");

            var myMsDataFile = new FakeMsDataFile(Scans);

            var oldFirstValue = myMsDataFile.GetOneBasedScan(1).MassSpectrum.FirstX;

            var secondScan = myMsDataFile.GetOneBasedScan(2) as IMsDataScanWithPrecursor <MzmlMzSpectrum>;

            Assert.AreEqual(1, secondScan.IsolationRange.Maximum - secondScan.IsolationRange.Minimum);

            MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, "argh.mzML", false);

            Mzml okay = Mzml.LoadAllStaticData(@"argh.mzML");

            okay.GetOneBasedScan(2);

            Assert.AreEqual(1, okay.GetClosestOneBasedSpectrumNumber(1));
            Assert.AreEqual(2, okay.GetClosestOneBasedSpectrumNumber(2));

            var newFirstValue = okay.GetOneBasedScan(1).MassSpectrum.FirstX;

            Assert.AreEqual(oldFirstValue.Value, newFirstValue.Value, 1e-9);

            var secondScan2 = okay.GetOneBasedScan(2) as IMsDataScanWithPrecursor <MzmlMzSpectrum>;

            Assert.AreEqual(1, secondScan2.IsolationRange.Maximum - secondScan2.IsolationRange.Minimum);

            secondScan2.MassSpectrum.ReplaceXbyApplyingFunction((a) => 44);
            Assert.AreEqual(44, secondScan2.MassSpectrum.LastX);
        }
Пример #6
0
        public void TestCoIsolation()
        {
            Peptide pep1 = new Peptide("AAAAAA");
            Peptide pep2 = new Peptide("AAA[H]AAA");

            var dist1 = IsotopicDistribution.GetDistribution(pep1.GetChemicalFormula(), 0.1, 0.01);

            var dist2 = IsotopicDistribution.GetDistribution(pep2.GetChemicalFormula(), 0.1, 0.01);

            MsDataScan[] Scans          = new MsDataScan[2];
            double[]     ms1intensities = new double[] { 0.8, 0.8, 0.2, 0.02, 0.2, 0.02 };
            double[]     ms1mzs         = dist1.Masses.Concat(dist2.Masses).OrderBy(b => b).Select(b => b.ToMz(1)).ToArray();

            double selectedIonMz = ms1mzs[1];

            MzSpectrum MS1 = new MzSpectrum(ms1mzs, ms1intensities, false);

            Scans[0] = new MsDataScan(MS1, 1, 1, false, Polarity.Positive, 1.0, new MzRange(300, 2000), "first spectrum", MZAnalyzerType.Unknown, MS1.SumOfAllY, null, null, null);

            // Horrible fragmentation, but we don't care about this!
            double[]   ms2intensities = new double[] { 1000 };
            double[]   ms2mzs         = new double[] { 1000 };
            MzSpectrum MS2            = new MzSpectrum(ms2mzs, ms2intensities, false);
            double     isolationMZ    = selectedIonMz;

            Scans[1] = new MsDataScan(MS2, 2, 2, false, Polarity.Positive, 2.0, new MzRange(100, 1500), "second spectrum", MZAnalyzerType.Unknown, MS2.SumOfAllY, null, null, null, selectedIonMz, null, null, isolationMZ, 2.5, DissociationType.HCD, 1, null);

            var myMsDataFile = new FakeMsDataFile(Scans);

            var cool = myMsDataFile.GetAllScansList().Last();

            int       maxAssumedChargeState = 1;
            Tolerance massTolerance         = Tolerance.ParseToleranceString("10 PPM");

            var isolatedMasses = cool.GetIsolatedMassesAndCharges(myMsDataFile.GetOneBasedScan(cool.OneBasedPrecursorScanNumber.Value).MassSpectrum, 1, maxAssumedChargeState, 10, 5).ToList();

            Assert.AreEqual(2, isolatedMasses.Count);
            Assert.AreEqual(2, isolatedMasses.Count(b => b.charge == 1));
            Assert.AreEqual(pep1.MonoisotopicMass, isolatedMasses.Select(b => b.peaks.First().Item1.ToMass(b.charge)).Min(), 1e-9);
            Assert.AreEqual(pep2.MonoisotopicMass, isolatedMasses.Select(b => b.peaks.First().Item1.ToMass(b.charge)).Max(), 1e-9);
            Assert.AreEqual(pep1.MonoisotopicMass, isolatedMasses.Select(b => b.monoisotopicMass.ToMz(b.charge).ToMass(b.charge)).Min(), 1e-9);
            Assert.AreEqual(pep2.MonoisotopicMass, isolatedMasses.Select(b => b.monoisotopicMass.ToMz(b.charge).ToMass(b.charge)).Max(), 1e-9);
        }
Пример #7
0
        public static void AnotherMzMLtest()
        {
            IMzmlScan[] scans = new IMzmlScan[4];

            double[]       intensities1 = new double[] { 1 };
            double[]       mz1          = new double[] { 50 };
            MzmlMzSpectrum massSpec1    = new MzmlMzSpectrum(mz1, intensities1, false);

            scans[0] = new MzmlScan(1, massSpec1, 1, true, Polarity.Positive, 1, new MzRange(1, 100), "f", MZAnalyzerType.Orbitrap, massSpec1.SumOfAllY, null, "1");

            double[]       intensities2 = new double[] { 1 };
            double[]       mz2          = new double[] { 30 };
            MzmlMzSpectrum massSpec2    = new MzmlMzSpectrum(mz2, intensities2, false);

            scans[1] = new MzmlScanWithPrecursor(2, massSpec2, 2, true, Polarity.Positive, 2, new MzRange(1, 100), "f", MZAnalyzerType.Orbitrap, massSpec2.SumOfAllY,
                                                 50, null, null, 50, 1, DissociationType.CID, 1, null, null, "2");

            double[]       intensities3 = new double[] { 1 };
            double[]       mz3          = new double[] { 50 };
            MzmlMzSpectrum massSpec3    = new MzmlMzSpectrum(mz3, intensities3, false);

            scans[2] = new MzmlScan(3, massSpec3, 1, true, Polarity.Positive, 1, new MzRange(1, 100), "f", MZAnalyzerType.Orbitrap, massSpec1.SumOfAllY, null, "3");

            double[]       intensities4 = new double[] { 1 };
            double[]       mz4          = new double[] { 30 };
            MzmlMzSpectrum massSpec4    = new MzmlMzSpectrum(mz4, intensities4, false);

            scans[3] = new MzmlScanWithPrecursor(4, massSpec4, 2, true, Polarity.Positive, 2, new MzRange(1, 100), "f", MZAnalyzerType.Orbitrap, massSpec2.SumOfAllY,
                                                 50, null, null, 50, 1, DissociationType.CID, 3, null, null, "4");

            FakeMsDataFile f = new FakeMsDataFile(scans);

            MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(f, Path.Combine(TestContext.CurrentContext.TestDirectory, "what.mzML"), false);

            Mzml ok = Mzml.LoadAllStaticData(Path.Combine(TestContext.CurrentContext.TestDirectory, "what.mzML"));

            var scanWithPrecursor = ok.Last(b => b is IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> >) as IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> >;

            Assert.AreEqual(3, scanWithPrecursor.OneBasedPrecursorScanNumber);
        }
Пример #8
0
        public void Setup()
        {
            Environment.CurrentDirectory = TestContext.CurrentContext.TestDirectory;

            UsefulProteomicsDatabases.Loaders.LoadElements();

            double[] mz          = { 328.73795, 329.23935, 447.73849, 448.23987, 482.23792, 482.57089, 482.90393, 500.95358, 501.28732, 501.62131, 611.99377, 612.32806, 612.66187, 722.85217, 723.35345 };
            double[] intensities = { 81007096.0, 28604418.0, 78353512.0, 39291696.0, 122781408.0, 94147520.0, 44238040.0, 71198680.0, 54184096.0, 21975364.0, 44514172.0, 43061628.0, 23599424.0, 56022696.0, 41019144.0 };

            _mzSpectrumA = new MzSpectrum(mz, intensities, false);

            var peptide = new Peptide("KQEEQMETEQQNKDEGK");

            MzSpectrum MS1 = CreateSpectrum(peptide.GetChemicalFormula(), 300, 2000, 1);
            MzSpectrum MS2 = CreateMS2spectrum(peptide.Fragment(FragmentTypes.b | FragmentTypes.y, true), 100, 1500);

            MsDataScan[] Scans = new MsDataScan[2];
            Scans[0] = new MsDataScan(MS1, 1, 1, false, Polarity.Positive, 1.0, new MzRange(300, 2000), "first spectrum", MZAnalyzerType.Unknown, MS1.SumOfAllY, 1, null, "scan=1");

            Scans[1] = new MsDataScan(MS2, 2, 2, false, Polarity.Positive, 2.0, new MzRange(100, 1500), "second spectrum", MZAnalyzerType.Unknown, MS2.SumOfAllY, 1, null, "scan=2", 693.9892, 3, .3872, 693.99, 1, DissociationType.Unknown, 1, 693.6550);

            myMsDataFile = new FakeMsDataFile(Scans);
        }
Пример #9
0
        [TestCase(1081.385183, 13, 35454636, 1081.385)]     //This is a lesser abundant charge state envelope at the high mz end
        public void TestDeconvolutionProteoformMultiChargeState(double selectedIonMz, int selectedIonChargeStateGuess, double selectedIonIntensity, double isolationMz)
        {
            MsDataScan[] Scans = new MsDataScan[1];

            //txt file, not mgf, because it's an MS1. Most intense proteoform has mass of ~14037.9 Da
            string Ms1SpectrumPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"DataFiles\14kDaProteoformMzIntensityMs1.txt");

            string[] spectrumLines = File.ReadAllLines(Ms1SpectrumPath);

            int mzIntensityPairsCount = spectrumLines.Length;

            double[] ms1mzs         = new double[mzIntensityPairsCount];
            double[] ms1intensities = new double[mzIntensityPairsCount];

            for (int i = 0; i < mzIntensityPairsCount; i++)
            {
                string[] pair = spectrumLines[i].Split('\t');
                ms1mzs[i]         = Convert.ToDouble(pair[0]);
                ms1intensities[i] = Convert.ToDouble(pair[1]);
            }

            MzSpectrum spectrum = new MzSpectrum(ms1mzs, ms1intensities, false);

            Scans[0] = new MsDataScan(spectrum, 1, 1, false, Polarity.Positive, 1.0, new MzRange(495, 1617), "first spectrum", MZAnalyzerType.Unknown, spectrum.SumOfAllY, null, null, null, selectedIonMz, selectedIonChargeStateGuess, selectedIonIntensity, isolationMz, 4);

            var myMsDataFile = new FakeMsDataFile(Scans);

            MsDataScan scan = myMsDataFile.GetAllScansList()[0];

            List <IsotopicEnvelope> isolatedMasses = scan.GetIsolatedMassesAndCharges(spectrum, 1, 60, 4, 3).ToList();

            List <double> monoIsotopicMasses = isolatedMasses.Select(m => m.MonoisotopicMass).ToList();

            //The primary monoisotopic mass should be the same regardless of which peak in which charge state was selected for isolation.
            //this case is interesting because other monoisotopic mass may have a sodium adduct. The unit test could be expanded to consider this.
            Assert.That(monoIsotopicMasses[0], Is.EqualTo(14037.926829).Within(.0005));
        }
Пример #10
0
        public static void TestCoIsolation()
        {
            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,
                },
                ConserveMemory = false,
                ScoreCutoff    = 1,
                DeconvolutionIntensityRatio = 50
            };

            var variableModifications = new List <ModificationWithMass>();
            var fixedModifications    = new List <ModificationWithMass>();
            var proteinList           = new List <Protein> {
                new Protein("MNNNKNDNK", null)
            };

            var searchModes = new SinglePpmAroundZeroSearchMode(5);

            Proteomics.Peptide pep1 = new Proteomics.Peptide("NNNK");
            Proteomics.Peptide pep2 = new Proteomics.Peptide("NDNK");

            var dist1 = IsotopicDistribution.GetDistribution(pep1.GetChemicalFormula(), 0.1, 0.01);

            var dist2 = IsotopicDistribution.GetDistribution(pep2.GetChemicalFormula(), 0.1, 0.01);

            IMzmlScan[] Scans          = new IMzmlScan[2];
            double[]    ms1intensities = new double[] { 0.8, 0.8, 0.2, 0.02, 0.2, 0.02 };
            double[]    ms1mzs         = dist1.Masses.Concat(dist2.Masses).OrderBy(b => b).Select(b => b.ToMz(1)).ToArray();

            double selectedIonMz = ms1mzs[1];

            MzmlMzSpectrum MS1 = new MzmlMzSpectrum(ms1mzs, ms1intensities, false);

            Scans[0] = new MzmlScan(1, MS1, 1, false, Polarity.Positive, 1.0, new MzRange(300, 2000), "first spectrum", MZAnalyzerType.Unknown, MS1.SumOfAllY, null, "scan=1");

            double[]       ms2intensities = new double[] { 1, 1, 1, 1, 1 };
            double[]       ms2mzs         = new double[] { 146.106.ToMz(1), 228.086.ToMz(1), 229.07.ToMz(1), 260.148.ToMz(1), 342.129.ToMz(1) };
            MzmlMzSpectrum MS2            = new MzmlMzSpectrum(ms2mzs, ms2intensities, false);
            double         isolationMZ    = selectedIonMz;

            Scans[1] = new MzmlScanWithPrecursor(2, MS2, 2, false, Polarity.Positive, 2.0, new MzRange(100, 1500), "second spectrum", MZAnalyzerType.Unknown, MS2.SumOfAllY, selectedIonMz, null, null, isolationMZ, 2.5, DissociationType.HCD, 1, null, null, "scan=2");

            var myMsDataFile = new FakeMsDataFile(Scans);

            bool      DoPrecursorDeconvolution           = true;
            bool      UseProvidedPrecursorInfo           = true;
            double    DeconvolutionIntensityRatio        = 50;
            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];

            List <ProductType> lp = new List <ProductType> {
                ProductType.B, ProductType.Y
            };

            new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, proteinList, lp, searchModes, false, CommonParameters, CommonParameters.ProductMassTolerance, new List <string>()).Run();

            // Two matches for this single scan! Corresponding to two co-isolated masses
            Assert.AreEqual(2, allPsmsArray.Length);

            Assert.IsTrue(allPsmsArray[0].Score > 1);
            Assert.AreEqual(2, allPsmsArray[0].ScanNumber);

            var ojdfkj = (SequencesToActualProteinPeptidesEngineResults) new SequencesToActualProteinPeptidesEngine(new List <PeptideSpectralMatch> {
                allPsmsArray[0], allPsmsArray[1]
            }, proteinList, fixedModifications, variableModifications, lp, new List <IDigestionParams> {
                CommonParameters.DigestionParams
            }, CommonParameters.ReportAllAmbiguity, new List <string>()).Run();

            foreach (var huh in allPsmsArray)
            {
                if (huh != null)
                {
                    huh.MatchToProteinLinkedPeptides(ojdfkj.CompactPeptideToProteinPeptideMatching);
                }
            }

            Assert.AreEqual("NNNK", allPsmsArray[0].BaseSequence);
            Assert.AreEqual("NDNK", allPsmsArray[1].BaseSequence);
        }