#CONF FRAGMENTS_FILE LTQ_ORBI_TRYP_fragments.txt
#CONF REGIONAL_FRAGMENT_SETS_FILE LTQ_ORBI_TRYP_fragment_sets.txt
#CONF MASS_SPEC_TYPE 1(currently only option 1) 
#CONF DIGEST_TYPE 1 (0 - non specific, 1 - trypsin)
#CONF MAX_NUMBER_OF_PEAKS_PER_LOCAL_WINDOW 12
#CONF NUMBER_OF_STRONG_PEAKS_PER_LOCAL_WINDOW 10
#CONF LOCAL_WINDOW_SIZE 200
#CONF TOLERANCE 0.01
#CONF PM_TOLERANCE 0.02
#CONF MAX_EDGE_LENGTH 3
#CONF TERMINAL_SCORE 12
#CONF NEED_TO_CORRECT_PM 0 (0 - no, 1 - yes)
#CONF TRY_MULTIPLE_PMS 0 (0 - no, 1 - yes)
#CONF SIZE_THRESHOLDS 6 0 0 0 0 0 0 
#CONF REGION_THRESHOLDS 2 0.225 0.775
