TaskType = "XLSearch"

[XlSearchParameters]
DecoyType = "Reverse"
CrosslinkSearchTopNum = 50
CrosslinkAtCleavageSite = true
WritePepXml = true
WriteOutputForPercolator = false
XlQuench_H2O = true
XlQuench_Tris = false
XlQuench_NH2 = false

[XlSearchParameters.Crosslinker]
CrosslinkerModSites = "KSTY"
CrosslinkerModSites2 = "KSTY"
CrosslinkerName = "DSS_KSTY"
Cleavable = true
CleaveDissociationTypes = []
TotalMass = 138.06808
CleaveMassShort = 0.0
CleaveMassLong = 0.0
LoopMass = 138.06808
DeadendMassH2O = 156.0786
DeadendMassNH2 = 155.0946
DeadendMassTris = 259.142

[CommonParameters]
TaskDescriptor = "DSS"
MaxThreadsToUsePerFile = 43
ListOfModsFixed = "Common Fixed\tCarbamidomethyl on C\t\tCommon Fixed\tCarbamidomethyl on U"
ListOfModsVariable = "Common Variable\tOxidation on M\t\tDSS\tDSS_hydro_K on K\t\tDSS\tDSS_hydro_Nt on X\t\tDSS\tDSS_hydro_S on S\t\tDSS\tDSS_hydro_T on T\t\tDSS\tDSS_hydro_Y on Y\t\tDSS\tDSS_loop_K on K\t\tDSS\tDSS_loop_Nt on X\t\tDSS\tDSS_loop_S on S\t\tDSS\tDSS_loop_T on T\t\tDSS\tDSS_loop_Y on Y"
DoPrecursorDeconvolution = true
UseProvidedPrecursorInfo = true
DeconvolutionIntensityRatio = 3.0
DeconvolutionMaxAssumedChargeState = 12
DeconvolutionMassTolerance = "±4.0000 PPM"
TotalPartitions = 1
ProductMassTolerance = "±20.0000 PPM"
PrecursorMassTolerance = "±10.0000 PPM"
AddCompIons = true
ScoreCutoff = 3.0
ReportAllAmbiguity = true
NumberOfPeaksToKeepPerWindow = 200
MinimumAllowedIntensityRatioToBasePeak = 0.01
NormalizePeaksAccrossAllWindows = false
TrimMs1Peaks = false
TrimMsMsPeaks = true
UseDeltaScore = false
QValueOutputFilter = 1.0
PepQValueOutputFilter = 1.0
CustomIons = []
AssumeOrphanPeaksAreZ1Fragments = true
MaxHeterozygousVariants = 4
MinVariantDepth = 1
AddTruncations = false
DissociationType = "HCD"
SeparationType = "HPLC"
MS2ChildScanDissociationType = "Unknown"
MS3ChildScanDissociationType = "Unknown"

[CommonParameters.DigestionParams]
MaxMissedCleavages = 3
InitiatorMethionineBehavior = "Variable"
MinPeptideLength = 5
MaxPeptideLength = 60
MaxModificationIsoforms = 1024
MaxModsForPeptide = 2
Protease = "trypsin"
SearchModeType = "Full"
FragmentationTerminus = "Both"
SpecificProtease = "trypsin"
GeneratehUnlabeledProteinsForSilac = true
KeepNGlycopeptide = false
KeepOGlycopeptide = false

[[FileSpecificParameters]]
[[FileSpecificParameters]]
[[FileSpecificParameters]]
[[FileSpecificParameters]]
