I don't see the differences in result from different research a concern. If the research is conducted in different environment with different samples the results will be of course different. You don't need to explain their results, you need to use your own result to support or contradict their results.
I'm not sure what proteomic studies in what articles you're referring to, but in addition to the sources of variation mentioned by the two colleagues above, I believe that there are large differences between two patients even with regard to the concentration of certain proteins, or their post-translational modification status, in biofluids, let alone between groups of patients stemming from different geographical locations and/or medical backgrounds/history.