The repeatability of the fractionation of the water-soluble extract (W
SE) of Cheddar cheese by gel permeation chromatography was assessed. T
he gel permeation profiles of the diafiltration permeates (DFP) obtain
ed from 5 commercial Cheddar cheeses varying in age from 5 to 33 month
s were very reproducible, showing some quantitative and qualitative di
fferences. Small fractions (10 ml) were collected from the gel permeat
ion chromatograms of the DFP. Analysis of the fractions by RP-HPLC sho
wed that the collection of 10 ml fractions gave a better separation of
some peptides than when larger fractions were pooled although it did
not offer a marked improvement for the isolation of individual peptide
s. The use of formic acid (50 mM) for the fractionation of cheese nitr
ogen was also studied. The preparation of a formic acid-soluble extrac
t (FASE) and especially the use of 50 mM formic acid as gel permeation
eluent gave a different fractionation of cheese peptides than that ob
tained with distilled water, mainly evident in the separation of a hig
her number of low molecular mass peptides. For a better assessment of
the fractionation, these peptides should be identified.