# Set paths to DAT files
-mdat /net/maccoss/vol2/software/bin/ISOTOPE.DAT
-hdat /net/maccoss/vol2/software/bin/Hardklor.dat

# Set global parameters
-d 2
-sn 2.5
-corr 0.99
-chMax 3
-res 60000 OrbiTrap
-a FewestPeptides
-cdm Q

# Files to analyze
#test
#note you can use local override flags
#in.ms1 in.out -corr 0.99