Profiling of urinary proteins by nano-high performance liquid chromatography/tandem mass spectrometry

There has been an increasing interest in proteomics which lies beyond the genomics era. Urine is one of the popular tools in proteomic field and has been the common focus to find proteins of interest, such as biomarkers, because urine is easy to collect and represents the body's status directly as does blood. To enhance our understanding of the urinary proteome, the water soluble urinary proteins were prepared in centrifuge filter tubes; one-dimensional gel electrophoresis (IDE) coupled nano-high performance liquid chromatography/tandem mass spectrometry (nano-LC/MS/MS) was used to profile the urinary proteins. From the male human urine profiled in this study, a total of 589 peptides, corresponding to 195 unique proteins, were identified by nano-LC/MS/MS. Each identified peptide's tandem mass spectrum was reconfirmed by manual verification. Some peptides-originated from oncogene family proteins, which may be potential biomarker candidates related to certain disease states. The protein profiling method using IDE coupled nano-LC/MS/MS showed sensitive, accurate, and unbiased protein identification. This technique will provide a powerful application tool for disease diagnosis and monitoring in the future clinic.