Short gel, long gradient liquid chromatography tandem mass spectrometry to investigate the urine proteome of chronic pancreatitis

Chronic pancreatitis (CP) is currently diagnosed using invasive endoscopic and imaging techniques. However, urine can be collected safely and noninvasively and as such may offer a superior alternative to current techniques of CP diagnosis. We use mass spectrometry-based methods to discover proteins which are exclusive to or differentially abundant in urine of chronic pancreatitis patients. We have performed a comparative quantitative proteomic analysis of urine collected from 5 healthy controls, 5 severe CP patients, and 5 patients of a mixed cohort with clinical representation typical of patients referred for CP, but not diagnosed with the disease. Proteins from urine were fractionated via SDS-PAGE and digested in-gel with trypsin prior to reversedphase liquid chromatography in-line with a mass spectrometer. ProteinPilot software and the QSPEC algorithm identified proteins and determined statistically significant differences between cohorts. We identified over 600 proteins from urine, of which several hundred were either exclusive to or differ quantitatively in severe CP patients. Members of the cathepsin protein family were of significantly higher abundance in the severe CP cohort. In addition, we have identified a core set of 50 proteins in all 15 samples, 25 of which showed no significant difference among the cohorts. The differentially abundant proteins in severe CP patients represent an initial set of targets for directed proteomics experiments for further validation studies.However, larger matched cohorts will be required to determine if these differences have statistically significant diagnostic potential.