I am conflicted about whether a patent that makes claims using general terms like "separation method" (without specifying enablement of each alternative method)
They do in fact specify specific enablements - e.g. claim 1 is using HPLC whereas claim 2 is the same but using FPLC, ...
The judge's question appears to be about the differentiation between 'determining' and 'separation method'. It is very hard to tell why this would matter without more context - the claims themselves talk of 'determination'. One possible guess would be:
a) The judge is not clear on how you 'determine' which fragment is which (the tables in the claims list different fragments - but how do you know which is which in a HPLC separation?)
b) ?
But I don't put a lot of faith in the above guess or any other guess without seeing more of the legal dialog.