Protein ID Fold change p-value Number of sample pairs Gene symbol Swiss-Prot accession number pI / mass (kDa) Score/ match Sequence coverage % 39S ribosomal protein L43, mitochondrial 134.8~246.1 0.0269 3 /5 MRPL43 Q8N983 8.97/23.8 619/400 22 Histone H4 10.5~22.9 0.0479 3 /5 HIST1H4A P62805 11.36/11.7 213/22 38 Annexin A1 2.6~13.9 0.0997 4 /5 ANXA1 P04083 6.57/39.9 560/47 39 Annexin A2 5.4~13.2 0.1362 3 /5 ANXA2 P07355 7.57/39.8 785/63 55 Keratin, type II cytoskeletal 8 5.2~10.3 0.0978 3 /5 KRT8 P05787 5.52/54.7 891/60 51 Histone H2A type 2-A 2.1~10.2 0.2082 3 /5 H2A2A Q6FI13 10.90/14.1 689/36 49 Vimentin 3.7~6.8 0.0209 4 /5 VIM P08670 5.06/54.3 11182/601 53 Filamin-A 2.6~6.5 0.0706 3 /5 FLNA P21333 5.70/288.4 425/165 32 Keratin, type I cytoskeletal 18 4.4~6.3 0.0822 3 /5 KRT18 P05783 5.34/48.7 1394/89 53 Tropomyosin alpha-1 chain 2.1~6.1 0.0443 4 /5 TPM1 P09493 4.69/34.0 87/46 38 Pyruvate kinase isozymes M1/M2 2.5~5.6 0.0220 4 /5 PKM2 P14618 7.96/59.7 3712/142 48 Ras GTPase-activating-like protein IQGAP1 2.6~5.3 0.1445 4 /5 IQGAP1 P46940 6.08/194.1 456/106 27 Galectin-1 3.3~5.3 0.0874 3 /5 LGALS1 P09382 5.34/15.3 82/13 68 Carbonic anhydrase 1 2.3~3.8 0.1208 3 /5 CA1 P00915 6.59/29.5 351/26 40 Transgelin 2.1~3.0 0.0047 4 /5 TAGLN Q01995 8.87/23.2 815/112 54 L-lactate dehydrogenase A chain 2.2~2.8 0.2245 3 /5 LDHA P00338 8.44/37.8 459/22 38 Annexin A4 2.5~2.8 0.0490 3 /5 ANXA4 P09525 5.84/36.2 953/25 35 Clathrin heavy chain 1 2.0~2.8 0.1907 3 /5 CLTC Q00610 5.48/196.3 994/114 30 D = Deuterium labeling (RCC tissues); H = Hydrogen labeling (normal tissues)

Table 1: Up-regulated proteins (D/H ratio ≥ 2) were displayed in at least three of five renal clear cell carcinoma (RCC) tissues analyzed by nano LC-MS/MS coupled with stable isotope dimethyl labeling.