Glycoproteins containing the mannose 6-phosphate (Man-6-P) modification 
represent a class of proteins of considerable biomedical importance. They 
include over sixty different soluble lysosomal hydrolases and accessory 
proteins, deficiencies of which result in over forty different known human 
genetic diseases. In addition, there are patients with lysosomal storage 
diseases of unknown etiology and lysosomal proteins have been implicated in 
pathophysiological processes associated with Alzheimer disease, arthritis, and 
cancer. The aim of this study was to explore urine as a source for the proteomic 
investigation of lysosomal storage disorders as well as for biomarker studies on 
the role of Man-6-P containing proteins in other human diseases. To this end, 
urinary proteins were affinity purified on immobilized Man-6-P receptors, 
digested with trypsin, and analyzed using nanospray LC/MS/MS. This resulted in 
identification of 67 proteins, including 48 known lysosomal proteins and 9 
proteins that may be lysosomal. The identification of a large proportion of the 
known set of soluble lysosomal proteins with relatively few contaminants 
suggests that urine represents a promising substrate for the development of 
comparative proteomic methods for the investigation of lysosomal disorders and 
other diseases involving Man-6-P glycoproteins.