-mdat <ISOTOPE.DAT file location>
-hdat <Hardklor.dat file location>

-d 3
-sn 1
-p 12
-corr 0.9
-chMax 5
-chMin 1
-res 50000 FTICR
-a FastFewestPeptides
-win 5.0
-snWin 250 1 
-cdm Q
-i
-sl 3

#Files to analyze
#<cms1 input file> <.hk output file name>
# example:
# 080720_S288C_4ug_1.cms1 080720_S288C_4ug_1_081023.hk
