idia.params

#DIA-Umpire (version 2.0)
#Data Independent Acquisition data processing and analysis package (Signal extraction module)

#No of threads
Thread = 8

#Fragment grouping parameter
RPmax = 25
RFmax = 300
CorrThreshold = 0.2
DeltaApex = 0.6
RTOverlap = 0.3
AdjustFragIntensity = true
BoostComplementaryIon = true

#Report peak
ExportPrecursorPeak = true
ExportFragmentPeak = true

#Signal extraction parameters
SE.MS1PPM = 30
SE.MS2PPM = 40
SE.SN = 2
SE.MS2SN = 2
SE.MinMSIntensity = 10
SE.MinMSMSIntensity = 10
SE.MaxCurveRTRange = 1
SE.Resolution = 17500
SE.StartCharge = 2
SE.EndCharge = 4
SE.MS2StartCharge = 2
SE.MS2EndCharge = 4
SE.NoMissedScan = 1
SE.MinFrag=10
SE.EstimateBG = true
SE.MinNoPeakCluster = 2
SE.MaxNoPeakCluster = 4
SE.StartRT = 0
SE.EndRT = 9999
SE.MinMZ = 200
SE.MinPrecursorMass = 200
SE.MaxPrecursorMass = 5000
SE.IsoPattern = 0.3
SE.MassDefectFilter = true
SE.MassDefectOffset = 0.1

#parameters of Gridmass
SE.MzTol = 0.01
SE.MinimumTimeSpan = 0.1
SE.MaximumTimeSpan = 5
SE.SmoothTimeMZ = 0.02
SE.SmoothMZ = 0.02

#combine isotopice traces from two methods
SE.SimilarityTwoMethods = 0.3

#Isolation window setting
#The current version supports the following window type: SWATH (fixed window size), V_SWATH (variable SWATH window)
WindowType=SWATH

#Fix window size (Only for Absciex SWATH data, for Thermo data, you don't need to change anything here.)
WindowSize=25

#Variable SWATH window setting (start m/z, end m/z, separated by Tab)
#The setting in this section will be used only if you specified WindowType=V_SWATH.
==window setting begin

==window setting end