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));
}
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();
}
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();
}
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;
}
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
};
}
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();
}
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();
}