From 913abd4af2fc0aa741ed88bc9967e42045ebbd86 Mon Sep 17 00:00:00 2001 From: trishorts Date: Fri, 13 Dec 2024 12:16:24 -0600 Subject: [PATCH] bug fix and unit test --- .../NonSpecificEnzymeSearchEngine.cs | 2 +- MetaMorpheus/Test/SearchEngineTests.cs | 23 + MetaMorpheus/Test/Test.csproj | 6 + .../Test/TestData/NonSpecificSearchToml.toml | 100 + .../Test/TestData/bosTaurusEnamPruned.xml | 5181 +++++++++++++++++ 5 files changed, 5311 insertions(+), 1 deletion(-) create mode 100644 MetaMorpheus/Test/TestData/NonSpecificSearchToml.toml create mode 100644 MetaMorpheus/Test/TestData/bosTaurusEnamPruned.xml diff --git a/MetaMorpheus/EngineLayer/NonSpecificEnzymeSearch/NonSpecificEnzymeSearchEngine.cs b/MetaMorpheus/EngineLayer/NonSpecificEnzymeSearch/NonSpecificEnzymeSearchEngine.cs index 4c23fa7d2..ff18c3c27 100644 --- a/MetaMorpheus/EngineLayer/NonSpecificEnzymeSearch/NonSpecificEnzymeSearchEngine.cs +++ b/MetaMorpheus/EngineLayer/NonSpecificEnzymeSearch/NonSpecificEnzymeSearchEngine.cs @@ -377,7 +377,7 @@ private Tuple Accepts(List fragments, updatedMods.Add(key, mod.Value); } } - if (terminalMod != null) + if (terminalMod != null && !updatedMods.Keys.Contains(startResidue - 1)) { updatedMods.Add(startResidue - 1, terminalMod); } diff --git a/MetaMorpheus/Test/SearchEngineTests.cs b/MetaMorpheus/Test/SearchEngineTests.cs index abc83c43a..7f7446c9d 100644 --- a/MetaMorpheus/Test/SearchEngineTests.cs +++ b/MetaMorpheus/Test/SearchEngineTests.cs @@ -979,6 +979,29 @@ public static void TestNonSpecificEnzymeSearchEngineSingleN() Assert.That(allPsmsArray[0].BaseSequence, Is.EqualTo("QQQGGGG")); } + [Test] + public static void TestNonSpecificEnzymeSearchEngine() + { + var myTomlPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\NonSpecificSearchToml.toml"); + var searchTaskLoaded = Toml.ReadFile(myTomlPath, MetaMorpheusTask.tomlConfig); + string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\NonSpecificSearchTest"); + Directory.CreateDirectory(outputFolder); + string myFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\TaGe_SA_A549_3_snip.mzML"); + string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\bosTaurusEnamPruned.xml"); + + var engineToml = new EverythingRunnerEngine(new List<(string, MetaMorpheusTask)> { ("SearchTOML", searchTaskLoaded) }, new List { myFile }, new List { new DbForTask(myDatabase, false) }, outputFolder); + engineToml.Run(); + + string psmFile = Path.Combine(outputFolder, @"SearchTOML\AllPSMs.psmtsv"); + + List parsedPsms = PsmTsvReader.ReadTsv(psmFile, out var warnings); + + Assert.That(parsedPsms.Count, Is.EqualTo(38)); //total psm count + + Directory.Delete(outputFolder, true); + + } + [Test] public static void TestNonSpecificEnzymeSearchEngineSingleNLowCID() diff --git a/MetaMorpheus/Test/Test.csproj b/MetaMorpheus/Test/Test.csproj index 3c3e7e879..3e111ba38 100644 --- a/MetaMorpheus/Test/Test.csproj +++ b/MetaMorpheus/Test/Test.csproj @@ -217,6 +217,9 @@ Always + + Always + Always @@ -325,6 +328,9 @@ Always + + Always + Always diff --git a/MetaMorpheus/Test/TestData/NonSpecificSearchToml.toml b/MetaMorpheus/Test/TestData/NonSpecificSearchToml.toml new file mode 100644 index 000000000..368d88329 --- /dev/null +++ b/MetaMorpheus/Test/TestData/NonSpecificSearchToml.toml @@ -0,0 +1,100 @@ +TaskType = "Search" + +[SearchParameters] +DisposeOfFileWhenDone = true +DoParsimony = true +ModPeptidesAreDifferent = false +NoOneHitWonders = false +MatchBetweenRuns = false +Normalize = false +QuantifyPpmTol = 5.0 +DoHistogramAnalysis = false +SearchTarget = true +DecoyType = "Reverse" +MassDiffAcceptorType = "OneMM" +WritePrunedDatabase = true +KeepAllUniprotMods = true +DoLocalizationAnalysis = false +DoLabelFreeQuantification = false +UseSharedPeptidesForLFQ = false +DoMultiplexQuantification = false +MultiplexModId = "TMT10" +DoSpectralRecovery = false +SearchType = "NonSpecific" +LocalFdrCategories = ["FullySpecific", "SemiSpecific", "NonSpecific"] +MaxFragmentSize = 10800.0 +MinAllowedInternalFragmentLength = 0 +HistogramBinTolInDaltons = 0.003 +MaximumMassThatFragmentIonScoreIsDoubled = 0.0 +WriteMzId = true +WritePepXml = false +WriteHighQValuePsms = true +WriteDecoys = true +WriteContaminants = true +WriteIndividualFiles = true +WriteSpectralLibrary = false +UpdateSpectralLibrary = false +CompressIndividualFiles = false +TCAmbiguity = "RemoveContaminant" +IncludeModMotifInMzid = false + +[SearchParameters.ModsToWriteSelection] +'N-linked glycosylation' = 3 +'O-linked glycosylation' = 3 +'Other glycosylation' = 3 +'Common Biological' = 3 +'Less Common' = 3 +Metal = 3 +'2+ nucleotide substitution' = 3 +'1 nucleotide substitution' = 3 +UniProt = 2 + +[CommonParameters] +TaskDescriptor = "SearchTask" +MaxThreadsToUsePerFile = 63 +ListOfModsFixed = "" +ListOfModsVariable = "Common Variable\tOxidation on M" +DoPrecursorDeconvolution = true +UseProvidedPrecursorInfo = true +DeconvolutionMaxAssumedChargeState = 12 +TotalPartitions = 1 +ProductMassTolerance = "±20.0000 PPM" +PrecursorMassTolerance = "±15.0000 PPM" +AddCompIons = true +QValueThreshold = 0.01 +PepQValueThreshold = 1.0 +ScoreCutoff = 5.0 +QValueCutoffForPepCalculation = 0.005 +ReportAllAmbiguity = true +NumberOfPeaksToKeepPerWindow = 200 +MinimumAllowedIntensityRatioToBasePeak = 0.01 +NormalizePeaksAccrossAllWindows = false +TrimMs1Peaks = false +TrimMsMsPeaks = true +CustomIons = [] +AssumeOrphanPeaksAreZ1Fragments = true +MaxHeterozygousVariants = 4 +MinVariantDepth = 1 +AddTruncations = false +DissociationType = "HCD" +SeparationType = "HPLC" +MS2ChildScanDissociationType = "Unknown" +MS3ChildScanDissociationType = "Unknown" +UseMostAbundantPrecursorIntensity = true + +[CommonParameters.DigestionParams] +InitiatorMethionineBehavior = "Variable" +MaxMissedCleavages = 35 +MaxModificationIsoforms = 1024 +SearchModeType = "None" +FragmentationTerminus = "C" +SpecificProtease = "singleC" +GeneratehUnlabeledProteinsForSilac = true +KeepNGlycopeptide = false +KeepOGlycopeptide = false +Protease = "singleC" +MinPeptideLength = 7 +MaxPeptideLength = 36 +MaxModsForPeptide = 2 + +[[FileSpecificParameters]] diff --git a/MetaMorpheus/Test/TestData/bosTaurusEnamPruned.xml b/MetaMorpheus/Test/TestData/bosTaurusEnamPruned.xml new file mode 100644 index 000000000..9a5508e6c --- /dev/null +++ b/MetaMorpheus/Test/TestData/bosTaurusEnamPruned.xml @@ -0,0 +1,5181 @@ + + + ID Acetylation on K +MT Common Biological +TG K +PP Anywhere. +CF C2H2O +MM 42.010564684 +DR Unimod; 1 +NL ETD:45.0204 +DI HCD:125.084063979 + +// + ID ADP-ribosylation on S +MT Common Biological +TG S +PP Anywhere. +CF C15H21N5O13P2 +MM 541.06110975 +DR Unimod; 213 + +// + ID Ammonia loss on N +MT Common Artifact +TG N +PP Anywhere. +CF H-3N-1 +MM -17.026549101 +DR Unimod; 385 + +// + ID Butyrylation on K +MT Common Biological +TG K +PP Anywhere. +CF C4H6O +MM 70.041864813 +DR Unimod; 1289 +DI HCD:153.115323533 + +// + ID Calcium on E +MT Metal +TG E +PP Anywhere. +CF H-2Ca +MM 37.946940799 +DR Unimod; 951 + +// + ID Carbamyl on K +MT Common Artifact +TG K +PP Anywhere. +CF CHNO +MM 43.005813656 +DR Unimod; 5 + +// + ID Carbamyl on M +MT Common Artifact +TG M +PP Anywhere. +CF CHNO +MM 43.005813656 +DR Unimod; 5 + +// + ID Carbamyl on R +MT Common Artifact +TG R +PP Anywhere. +CF CHNO +MM 43.005813656 +DR Unimod; 5 + +// + ID Carbamyl on X +MT Common Artifact +TG X +PP Peptide N-terminal. +CF CHNO +MM 43.005813656 +DR Unimod; 5 + +// + ID Carboxylation on D +MT Common Biological +TG D +PP Anywhere. +CF CO2 +MM 43.989829239 +DR Unimod; 299 + +// + ID Carboxylation on E +MT Common Biological +TG E +PP Anywhere. +CF CO2 +MM 43.989829239 +DR Unimod; 299 + +// + ID Carboxylation on K +MT Common Biological +TG K +PP Anywhere. +CF CO2 +MM 43.989829239 +DR Unimod; 299 + +// + ID Citrullination on R +MT Common Biological +TG R +PP Anywhere. +CF H-1N-1O +MM 0.984015583 +DR Unimod; 7 +NL HCD:43.0058 +DI HCD:129.090223533 + +// + ID Cu[I] on D +MT Metal +TG D +PP Anywhere. +CF H-1Cu +MM 61.921772688 +DR Unimod; 531 + +// + ID Cu[I] on E +MT Metal +TG E +PP Anywhere. +CF H-1Cu +MM 61.921772688 +DR Unimod; 531 + +// + ID Deamidation on N +MT Common Artifact +TG N +PP Anywhere. +CF H-1N-1O +MM 0.984015583 +DR Unimod; 7 + +// + ID Deamidation on Q +MT Common Artifact +TG Q +PP Anywhere. +CF H-1N-1O +MM 0.984015583 +DR Unimod; 7 + +// + ID Dimethylation on K +MT Common Biological +TG K +PP Anywhere. +CF C2H4 +MM 28.031300129 +DR Unimod; 36 + +// + ID Dimethylation on R +MT Common Biological +TG R +PP Anywhere. +CF C2H4 +MM 28.031300129 +DR Unimod; 36 +NL ETD:31.0422 or ETD:45.0579 + +// + ID Fe[II] on D +MT Metal +TG D +PP Anywhere. +CF H-2Fe +MM 53.919286266 +DR Unimod; 952 + +// + ID Fe[II] on E +MT Metal +TG E +PP Anywhere. +CF H-2Fe +MM 53.919286266 +DR Unimod; 952 + +// + ID Formylation on K +MT Common Biological +TG K +PP Anywhere. +CF CO +MM 27.99491462 +DR Unimod; 122 +DI HCD:111.068423533 + +// + ID Glutarylation on K +MT Common Biological +TG K +PP Anywhere. +CF C5H6O3 +MM 114.031694052 +DR Unimod; 1848 +NL ETD:115.0395 +DI HCD:181.110323533 + +// + ID HexNAc on Nxs +MT Common Biological +TG Nxs +PP Anywhere. +CF C8H13NO5 +MM 203.079372521 +DR Unimod; 43 +NL AnyActivationType:203.079372521 + +// + ID HexNAc on S +MT Common Biological +TG S +PP Anywhere. +CF C8H13NO5 +MM 203.079372521 +DR Unimod; 43 +NL AnyActivationType:203.079372521 + +// + ID HexNAc on T +MT Common Biological +TG T +PP Anywhere. +CF C8H13NO5 +MM 203.079372521 +DR Unimod; 43 +NL AnyActivationType:203.079372521 + +// + ID Hydroxybutyrylation on K +MT Common Biological +TG K +PP Anywhere. +CF C4H6O2 +MM 86.036779433 +DI HCD:169.110323533 + +// + ID Hydroxylation on K +MT Common Biological +TG K +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Hydroxylation on N +MT Common Biological +TG N +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 + +// + ID Hydroxylation on P +MT Common Biological +TG P +PP Anywhere. +CF O +MM 15.99491462 +DR Unimod; 35 +DI HCD:170.069143 + +// + ID Magnesium on D +MT Metal +TG D +PP Anywhere. +CF H-2Mg +MM 21.969391633 +DR Unimod; 956 + +// + ID Magnesium on E +MT Metal +TG E +PP Anywhere. +CF H-2Mg +MM 21.969391633 +DR Unimod; 956 + +// + ID Malonylation on K +MT Common Biological +TG K +PP Anywhere. +CF C3H2O3 +MM 86.000393923 +DR Unimod; 747 +NL ETD:87.0082 +NL HCD:43.9898 +DI HCD:125.084063979 or HCD:169.073923533 + +// + ID Methylation on K +MT Common Biological +TG K +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Methylation on R +MT Common Biological +TG R +PP Anywhere. +CF CH2 +MM 14.015650064 +DR Unimod; 34 + +// + ID Phosphorylation on S +MT Common Biological +TG S +PP Anywhere. +CF HO3P +MM 79.966330889 +DR Unimod; 21 +NL HCD:0 or HCD:97.976895573 + +// + ID Phosphorylation on T +MT Common Biological +TG T +PP Anywhere. +CF HO3P +MM 79.966330889 +DR Unimod; 21 +NL HCD:0 or HCD:97.976895573 + +// + ID Phosphorylation on Y +MT Common Biological +TG Y +PP Anywhere. +CF HO3P +MM 79.966330889 +DR Unimod; 21 +NL HCD:0 or HCD:97.976895573 +DI HCD:215.034744803 + +// + ID Potassium on E +MT Metal +TG E +PP Anywhere. +CF H-1K +MM 37.955881454 +DR Unimod; 530 + +// + ID Pyridoxal phosphate on K +MT Common Biological +TG K +PP Anywhere. +CF C8H8NO5P +MM 229.014009359 +DR Unimod; 46 + +// + ID Sodium on D +MT Metal +TG D +PP Anywhere. +CF H-1Na +MM 21.98194425 +DR Unimod; 30 + +// + ID Sodium on E +MT Metal +TG E +PP Anywhere. +CF H-1Na +MM 21.98194425 +DR Unimod; 30 + +// + ID Succinylation on K +MT Common Biological +TG K +PP Anywhere. +CF C4H4O3 +MM 100.016043988 +DR Unimod; 64 +NL ETD:101.0239 +DI HCD:183.089523533 + +// + ID Sulfonation on Y +MT Common Biological +TG Y +PP Anywhere. +CF O3S +MM 79.956815033 +DR Unimod; 40 +NL AnyActivationType:79.956815033 + +// + ID Trimethylation on K +MT Common Biological +TG K +PP Anywhere. +CF C3H6 +MM 42.046950193 +DR 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