Normal Tissue Primary Tissue Metastatic Tissue Highest in Normal peptide # Spectral Count peptide # Spectral Count peptide # Spectral Count Alpha-2-macroglobulin 36 410 23 101 28 188 Serotransferrin 36 260 18 80 27 185 Serum albumin 28 192 10 33 18 70 Hemopexin 18 191 11 38 10 75 Alpha-1-antitrypsin 1-1 10 186 8 65 7 74 Alpha-1-antitrypsin 1-2 9 186 7 73 5 85 Alpha-1-antitrypsin 1-4 8 159 7 70 6 51 Complement C3 35 132 17 36 30 69 Murinoglobulin-1 28 128 20 55 22 52 Apolipoprotein A-I 17 123 5 31 7 39 Plasminogen 22 72 7 7 8 11 Haptoglobin 11 65 3 3 6 15 Apolipoprotein A-II 4 63 3 19 4 15 Fibronectin 28 62 13 17 18 23 Liver carboxylesterase N 12 59 5 10 8 11 Alpha-2-HS-glycoprotein 6 59 5 15 6 38 Apolipoprotein C-III 3 58 2 19 3 16 Complement factor H 24 57 8 9 13 16 Kininogen-1 13 36 6 8 12 17 Vitamin D-binding protein 13 32 7 8 12 24 Apolipoprotein E 7 31 4 5 5 8 Inter-alpha-trypsin inhibitor heavy chain H3 10 28 5 5 10 16 Fetuin-B 6 28 3 5 4 8 Antithrombin-III 14 24 5 5 9 10 Afamin 9 19 3 4 7 8 Serine protease inhibitor A3N 9 16 3 7 4 14 Complement factor B 11 15 5 5 7 8 Vitronectin 8 15 2 3 4 9 Gelsolin 8 13 4 4 4 4 Prothrombin 8 12 4 5 4 4 Inter-alpha-trypsin inhibitor heavy chain H1 8 12 7 9 4 7 Clusterin 8 11 ND ND 3 4 Plasma kallikrein 8 10 4 4 4 4 Carboxypeptidase N catalytic chain 7 10 2 2 2 2 Corticosteroid-binding globulin 6 8 ND ND 4 4 Carboxypeptidase N subunit 2 4 8 3 4 3 4 Complement factor I 7 8 3 4 5 6 Serum paraoxonase/arylesterase 1 4 7 ND ND 2 2 Serum amyloid A-1 protein 3 5 ND ND 3 3 Heparin cofactor 2 4 5 3 3 2 3 C4b-binding protein 3 4 ND ND 3 4 Coagulation factor X 3 4 2 2 ND ND Highest in Non-Met Tumor Serine protease inhibitor A3M 8 61 7 243 6 51 Serine protease inhibitor A3K 15 75 15 125 13 74 Highest in Metastatic Ceruloplasmin 27 96 10 18 27 98 Apolipoprotein A-IV 8 18 5 40 9 69 Alpha-1-acid glycoprotein 1 3 35 3 5 5 36 Hemoglobin subunit alpha 2 7 4 16 4 33 Complement C4-B 8 11 5 6 6 19 Inter-alpha-trypsin inhibitor heavy chain H2 5 6 3 5 7 12 Hemoglobin subunit beta-1 4 6 3 7 4 10

Table 2: Spectral count and peptide number analysis of serum circulating human proteins obtained from pooled humanized ccRCC mouse tumor model systems. Pooled mouse sera (n=5/group) from each of the three tissue explant groups were first depleted of albumin and immunoglobulins by a ProteoPrep AI spin column (Sigma-Aldrich). Following overnight trypsin digestion, peptides were analyzed using a 4-cycle automated two dimensional MudPIT separation on an LTQ Orbitrap-XL mass spectrometer as previously described [103]. Protein identifications were accepted if they could be established at greater than 95.0% probability and contained at least 2 identified peptides per analyzed sample. Raw data was converted to m/z XML and searched by SEQUEST against a human or mouse IPI protein sequence database. Results are presented as the most abundantly expressed detected serum proteins in mice implanted with normal kidney tissue, primary ccRCC tumor tissue, or metastatic tumor tissue. Peptide numbers represent the number of individual peptides detected for each protein species, and the spectral count number represents the cumulative number of times a peptide from a given protein was detected across the chromatography run.