示例#1
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        public NeoSearchTask() : base(MyTask.Neo)
        {
            NeoParameters = new NeoParameters();
            var tempDigParams = new DigestionParams(protease: "non-specific", maxMissedCleavages: 12, minPeptideLength: 8, maxPeptideLength: 13);

            CommonParameters = new CommonParameters(
                digestionParams: tempDigParams,
                doPrecursorDeconvolution: false,
                precursorMassTolerance: new PpmTolerance(double.MaxValue),
                productMassTolerance: new PpmTolerance(double.MaxValue));
        }
示例#2
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        public XLSearchTask() : base(MyTask.XLSearch)
        {
            var digestPara = new DigestionParams(
                minPeptideLength: 5
                );

            CommonParameters = new CommonParameters(
                precursorMassTolerance: new PpmTolerance(10),
                scoreCutoff: 3,
                trimMsMsPeaks: false,
                digestionParams: digestPara
                );

            XlSearchParameters = new XlSearchParameters();
        }
示例#3
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        public XLSearchTask() : base(MyTask.XLSearch)
        {
            //Default parameter setting which is different from SearchTask, can be overwriten
            var digestPara = new DigestionParams(
                minPeptideLength: 5
                );

            CommonParameters = new CommonParameters(
                precursorMassTolerance: new PpmTolerance(10),
                scoreCutoff: 3,
                trimMsMsPeaks: false,
                digestionParams: digestPara
                );

            XlSearchParameters = new XlSearchParameters();
        }
示例#4
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        public CommonParameters()
        {
            ProductMassTolerance   = new PpmTolerance(20);
            PrecursorMassTolerance = new PpmTolerance(5);

            DigestionParams = new DigestionParams();

            BIons    = true;
            YIons    = true;
            ZdotIons = false;
            CIons    = false;

            TotalPartitions = 1;
            LocalizeAll     = true;

            ListOfModsVariable = new List <(string, string)> {
                ("Common Variable", "Oxidation of M")
            };
            ListOfModsFixed = new List <(string, string)> {
                ("Common Fixed", "Carbamidomethyl of C"), ("Common Fixed", "Carbamidomethyl of U")
            };
            ListOfModTypesLocalize = new List <string>();

            ConserveMemory = true;

            MaxParallelFilesToAnalyze = 1;

            MaxThreadsToUsePerFile = Environment.ProcessorCount > 1 ? Environment.ProcessorCount - 1 : 1;

            ScoreCutoff = 5;

            // Deconvolution stuff
            DoPrecursorDeconvolution           = true;
            UseProvidedPrecursorInfo           = true;
            DeconvolutionIntensityRatio        = 3;
            DeconvolutionMaxAssumedChargeState = 12;
            DeconvolutionMassTolerance         = new PpmTolerance(4);
            ReportAllAmbiguity = true;

            TopNpeaks       = 200;
            MinRatio        = 0.01;
            TrimMs1Peaks    = false;
            TrimMsMsPeaks   = true;
            CalculateEValue = false;
        }
示例#5
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        public NeoSearchTask() : base(MyTask.Neo)
        {
            NeoParameters = new NeoParameters();

            IDigestionParams tempDigParams = new DigestionParams
            {
                MinPeptideLength   = 8,
                MaxPeptideLength   = 13,
                Protease           = GlobalVariables.ProteaseDictionary["non-specific"],
                MaxMissedCleavages = 12
            };

            CommonParameters = new CommonParameters
            {
                DigestionParams          = tempDigParams,
                DoPrecursorDeconvolution = false,
                PrecursorMassTolerance   = null,
                ProductMassTolerance     = null
            };
        }
示例#6
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        public XLSearchTask() : base(MyTask.XLSearch)
        {
            //Default parameter setting which is different from SearchTask, can be overwriten here.
            //maxMissedCleavage is set to 3 for crosslink generally induce long peptides.
            //maxPeptideLength is set to 60 in case generate peptides that are too long.
            //numberOfPeaksToKeepPerWindow is set to a large number to keep all peak with intensity > 0.01.
            var digestPara = new DigestionParams(
                minPeptideLength: 5,
                maxPeptideLength: 60,
                maxMissedCleavages: 3
                );

            CommonParameters = new CommonParameters(
                precursorMassTolerance: new PpmTolerance(10),
                scoreCutoff: 2,
                numberOfPeaksToKeepPerWindow: 1000,
                digestionParams: digestPara
                );

            XlSearchParameters = new XlSearchParameters();
        }
示例#7
0
        public GlycoSearchTask() : base(MyTask.GlycoSearch)
        {
            //Default parameter setting which is different from SearchTask, can be overwriten
            var digestPara = new DigestionParams(
                minPeptideLength: 5,
                maxPeptideLength: 60

                );

            CommonParameters = new CommonParameters(
                precursorMassTolerance: new PpmTolerance(10),
                ms2childScanDissociationType: DissociationType.EThcD,
                scoreCutoff: 3,
                trimMsMsPeaks: false,
                numberOfPeaksToKeepPerWindow: 1000,
                minimumAllowedIntensityRatioToBasePeak: 0.01,
                digestionParams: digestPara

                );

            _glycoSearchParameters = new GlycoSearchParameters();
        }