Practical bioinformatics for proteomics

We used various bioinformatic tools to examine the unknown protein gi|12841975 that was up-regulated in mouse diabetic kidneys. The data indicate that this unknown protein is, indeed, the PEBP. Motif scanning showed that this protein contains several kinase motifs, especially PKC that plays an important role in the pathogenesis of diabetic nephropathy [24, 25]. We therefore hypothesize that this protein (PEBP) has a potential functional role in PKC-dependent pathogenic pathways of diabetic nephropathy. Further study will be focused on phosphorylation pathways of the PEBP and its substrates. In summary, we have presented a case study that outlines our approach to further characterize the unknown proteins identified by peptide mass fingerprinting. Publicly accessible bioinformatic tools can provide a wealth of information to guide subsequent approaches that use traditional molecular biology tools.