Urine is a desirable material for the diagnosis and classification of diseases due to the convenience of collection in large amounts, however any of the urinary proteome catalogs currently being generated have limitations in their depth and confidence of identification. Our laboratory has developed methods involving a linear ion trap - Fourier transform (LTQ-FT) and a linear ion trap - orbitrap (LTQ-Orbitrap) mass spectrometer for the in-depth characterization of body fluids. Here we applied these methods to the analysis of the human urinary proteome.
	We employed one-dimensional SDS-PAGE and reverse phase HPLC for protein separation and fractionation. Fractionated proteins were digested in-gel or in-solution and digests were analyzed with the LTQ-FT and LTQ-Orbitrap at p.p.m. accuracy and with two consecutive stages of mass spectrometric fragmentation. We identified 1543 proteins in the urine obtained from ten healthy donors, while essentially eliminating false positive identifications. Surprisingly, nearly half of the annotated proteins were membrane proteins according to Gene ontology (GO) analysis. Furthermore, extracellular, lysosomal and plasma membrane proteins were enriched in the urine compared with all GO entries. Plasma membrane proteins are likely present in urine by secretion in exosomes.
	Our analysis provides a high confidence set of proteins present in human urinary proteome and provides a useful reference for comparing datasets obtained with different methodologies. The urinary proteome is unexpectedly complex and may prove useful in biomarker discovery in the future.
	This database accompanies the article: Adachi J., Kumar C., Zhang Y., Olsen J.V., Mann M., The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins, Genome Biol.;7(9):R80. (2006)