Great tool! I was hoping you could explain an issue I am having.
I have imported K602 and R604 SILAC labeled data and have confident library assignments for my target peptides (green circles). For K602 labeled peptides there is a total ratio provided after the dot product. However, this information is not provided next to R604 labeled peptides. Peptide settings -> Modifications have been set up so that a 'HeavyR' Isotope label type is associated with the 'Label: 13C(6) 15N(4) (C-term R)' Isotope modification and accordingly for 'HeavyK' and 'nolabel' isotope label types. Please let me know if there is anything else that I can provide.
p.s. Does total ratio refer to the light/heavy ratio?