Glomerular diseases are leading causes of end-stage renal diseases worldwide. They are considered to be consequences of injury primarily to the three types of glomerular cells. Differential diagnosis typically relies an invasive biopsy findings. We expected that injuries of different glomerular cells would cause different changes in urinary proteome. The goal of this study was to identify differential urinary proteins distinguishing between injuries of different glomerular cells before significant histopathologic changes. Adriamycin nephropathy and Thy1.1 glomerulonephritis were employed as models with different primary impaired cells. ConA-enriched urinary glycoproteome on day3 were profiled by gel-free shotgun tandem mass spectrometry, and compared with self-healthy controls to identify differential urinary proteins for each model. By comparing the changes of the differential proteins between these two models, we identified 39 proteins with different directions of changes, which may potentially be useful in differentiation; and 7 proteins with the same direction of changes, which may be potential indicators of early renal damage. These differential proteins were of several origins: plasma proteins, proteins with urine or kidney specificity, proteins without tissue-specificity (mainly inflammatory mediators) etc. Our results may help better understand the effects of injuries of different glomerular cells at the initial stage, and lead to the discovery of novel early diagnostic markers for human focal segmental glomerulosclerosis (FSGS) and mesangioproliferative glomerulonephritis (MsPGN) which have the same primary impaired cells with adriamycin nephropathy and Thy1.1 glomerulonephritis, respectively. (C) 2008 Elsevier Inc. All rights reserved.