TaskType = "GlycoSearch"

[_glycoSearchParameters]
OGlycanDatabasefile = "OGlycan.gdb"
NGlycanDatabasefile = "NGlycan182.gdb"
GlycoSearchType = "OGlycanSearch"
OxoniumIonFilt = true
DecoyType = "Reverse"
GlycoSearchTopNum = 50
MaximumOGlycanAllowed = 4

[CommonParameters]
TaskDescriptor = "GlycoSearchTask"
MaxThreadsToUsePerFile = 7
ListOfModsFixed = "Common Fixed\tCarbamidomethyl on C\t\tCommon Fixed\tCarbamidomethyl on U"
ListOfModsVariable = "Common Variable\tOxidation on M"
DoPrecursorDeconvolution = true
UseProvidedPrecursorInfo = true
DeconvolutionIntensityRatio = 3.0
DeconvolutionMaxAssumedChargeState = 12
DeconvolutionMassTolerance = "±4.0000 PPM"
TotalPartitions = 1
ProductMassTolerance = "±20.0000 PPM"
PrecursorMassTolerance = "±10.0000 PPM"
AddCompIons = false
ScoreCutoff = 3.0
ReportAllAmbiguity = true
NumberOfPeaksToKeepPerWindow = 1000
MinimumAllowedIntensityRatioToBasePeak = 0.01
NormalizePeaksAccrossAllWindows = false
TrimMs1Peaks = false
TrimMsMsPeaks = false
UseDeltaScore = false
QValueOutputFilter = 1.0
CustomIons = []
AssumeOrphanPeaksAreZ1Fragments = true
MaxHeterozygousVariants = 4
MinVariantDepth = 1
DissociationType = "HCD"
SeparationType = "HPLC"
MS2ChildScanDissociationType = "EThcD"
MS3ChildScanDissociationType = "Unknown"

[CommonParameters.DigestionParams]
MaxMissedCleavages = 2
InitiatorMethionineBehavior = "Variable"
MinPeptideLength = 5
MaxPeptideLength = 60
MaxModificationIsoforms = 1024
MaxModsForPeptide = 2
Protease = "trypsin"
SearchModeType = "Full"
FragmentationTerminus = "Both"
SpecificProtease = "trypsin"
GeneratehUnlabeledProteinsForSilac = true
KeepNGlycopeptide = false
KeepOGlycopeptide = false