### 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