Characterization of the protein profile of the whey fraction from a milk sample taken from an individual donkey belonging to the 'Ragusana' species of the East of Sicily is reported. Direct RP-HPLC/electrospray ionization (ESI)-MS analysis of the whey fraction allowed the detection of some unknown components, together with the identification of already known whey proteins. Matrix-assisted laser desorption/ionization (MALDI)-TOF/MS and RP-HPLC/ESI-MS/MS analysis of the enzymatic digests of the unknown components resulted the identification and characterization of (1) two beta-casein fragments; (2) the sequence of donkey's serum albumin; and (3) the oxidized methionine forms of lysozyme B and alpha-lactoalbumin. One of the two beta-casein fragments corresponds to the sequence Val(176)-Arg(189) of the horse's beta-casein. The second one corresponds the C-terminal sequence Tyr(199)-Val(226) of the horse's beta-casein, with four amino acid substitutions (Q --> R(203), L/I --> P(206), F --> L(210) and P --> A(219)). Both fragments, reasonably arising by endogenous proteases cleavage of the donkey's beta-casein, could be potential biologically active peptides. Direct mass spectrometric sequence characterization of the detected donkey's serum albumin reveals the presence of the amino acid substitution Val --> Ile at position 497 with respect to the cDNA deduced sequence. The oxidized forms of lysozyme B and alpha-lactoalbumin are selectively oxidized at methionine 79 and methionine 90, respectively.