A recent publication in the Journal of Proteome Research applied metabolic profiling ("metabonomics") to ulcerative colitis; several different biosamples were investigated ( J. Proteome Res. 2010 , 9 , 954 - 962 ). Comparing urinary profiles, no differences were found between cases and controls; in a previously published study ( Am. J. Gastroenterol. 2009 , 104 , 1435 - 1444 ), we had found significant differences. In this correspondence, the reasons for our experimental and analytical approach are explained, and the negative results of the Journal of Proteome Research study are discussed.