Protein Name Stage 1 Stage 2 Stage 3 Stage4 N T N T N T N T Aldolase B 53 ND 45 ND 85 ND 79 39 Gamma Enolase ND 63 ND 12 ND 46 ND 29 Adipophilin ND 63 ND 12 ND 46 ND 29 TGF-beta induced 23 107 14 12 12 36 11 20 Vimentin 107 168 60 62 96 189 201 271 Isocitrate DH 11 3 11 2 11 ND 8 3 Gelsolin 11 13 12 2 8 7 8 12 Ceruloplasmin 9 10 9 6 3 8 12 16

Table 1: Selected expression of putative ccRCC protein biomarkers in pooled normal (N) and tumor (T) tissues representative of Stage 1-4 cancers. Individual renal tissues (10-15 mg) from matched tumor and normal pairs were processed by trifluoroethanol (TFE) solubilization and sonication as adapted from Wang et al. [104]. Following trypsin digestion, the resulting peptides were separated by MudPIT and analyzed for protein identification as described in the legend to Table 2. Results are listed as spectral counts for each indicated protein.