### default parameters

# verbose mode
quiet=false
# toggle the mz computation mode to AVERAGE if true
average=false
# set the number of fraction digits (real number format)
precision=2
# the tolerance for spectrum matching
tol=0.1
# the fragments
frags=b,y
# en/disable neutral loss fragmentation.
loss=false
# set the PeptideSpectrumMatch (PSM) filter inequation expression
filter=peptideprophet >= 0.75
# en/disable the phosphate rule losses
loss-phosphate=false
# en/disable the water/ammonium losses
loss=false
# maximum number of simultaneous loss sites
max-loss-sites=2
