Protein ID Fold change p-value Number of sample pairs Gene symbol Swiss-Prot accession number pI/mass (kDa) Score/match Sequence coverage %
Enoyl-CoA hydratase, mitochondrial 15.8~23.1 <0.001* 5 /5 ECHS1 P30084 8.34/32.5 1267/51 37
Phosphoenolpyruvatecarboxykinase [GTP], mitochondrial 13.5~60.0 <0.001* 5 /5 PCK2 Q16822 7.57/72.1 53/28 23
Argininosuccinate synthase 13.3~37.7 0.409 3 /5 ASS1 P00966 8.08/47.8 664/35 54
Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial 9.9~17.5 <0.001* 5 /5 ALDH4A1 P30038 8.25/63.1 2221/100 27
Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial 8.7~27.7 0.854 3 /5 ALDH6A1 Q02252 8.72/59.2 485/44 51
Glycine amidinotransferase, mitochondrial 8.3~24.5 <0.001* 5 /5 GATM P50440 8. 26/49.6 415/33 39
Bifunctional ATP-dependent dihydroxyacetone kinase/FAD-AMP lyase (cyclizing) 7.7~18.4 0.347 3 /5 DAK Q3LXA3 7.12/59.2 188/28 38
Ribonuclease UK114 6.9~29.1 0.001 3 /5 HRSP12 P52758 8.74/14.8 156/14 37
Dihydropyrimidinase 6.6~38.4 0.002 3 /5 DPYS Q14117 6.81/58.1 505/19 27
Betaine--homocysteine S-methyltransferase 1 6.2~18.2 0.963 4 /5 BHMT Q93088 6.58/46.3 892/39 38
Calbindin 6.0~48.6 0.005 4 /5 CALB1 P05937 4.70/31.0 158/13 29
Fructose-bisphosphatealdolase B 5.3~25.3 <0.001* 5 /5 ALDOB P05062 8.00/40.6 1592/160 73
Aromatic-L-amino-acid decarboxylase 4.9~21.9 <0.001* 4 /5 DDC P20711 6.77/55.2 68/15 19
3-ketoacyl-CoA thiolase, mitochondrial 4.8~6.3 0.514 3 /5 ACAA2 P42765 8.32/43.1 191/35 41
Ketohexokinase 4.6~26.6 0.299 4 /5 KHK P50053 5.64/33.5 622/111 21
Aminoacylase-1 4.3~30.8 <0.001* 4 /5 ACY1 Q03154 5.77/46.5 102/23 43
Xaa-Pro dipeptidase 4.3~23.7 0.006 3 /5 PEPD P12955 5.64/55.8 151/24 28
L-xylulosereductase 4.1~12.3 <0.001* 4 /5 DCXR Q7Z4W1 8.33/26.4 635/23 36
Hydroxymethylglutaryl-CoA lyase, mitochondrial 4.0~5.7 0.596 3 /5 HMGCL P35914 8.81/35.4 142/48 28
Mu-crystallin homolog 3.8~23.7 <0.001* 4 /5 CRYM Q14894 5.06/34.4 437/14 40
3-ketoacyl-CoA thiolase, peroxisomal 3.6~22.7 0.883 3 /5 ACAA1 P09110 8.76/45.4 874/35 49
Vitamin D-binding protein 3.4~4.9 0.028 3 /5 GC P02774 5.40/54.5 145/14 17
Glutathione S-transferase A1 3.3~50.6 <0.001* 5 /5 GSTA1 P08263 8.91/26.3 802/84 67
Medium-chain specific acyl-CoA dehydrogenase, mitochondrial 3.2~9.6 <0.001* 4 /5 ACADM P11310 8.61/47.8 130/13 31
Sodium/potassium-transporting ATPase subunit alpha-1 3.2~7.6 0.567 3 /5 ATP1A1 P05023 5.33/115.9 575/50 19
Aconitatehydratase, mitochondrial 2.5~35.0 0.003 4 /5 ACO2 Q99798 7.36/87.7 313/49 27
Fructose-1,6-bisphosphatase 1 3.0~29.6 0.738 3 /5 FBP1 P09467 6.54/38.0 469/26 36
Transthyretin 5.4~9.4 <0.001* 4 /5 TTR P02766 5.52/16.2 610/54 49
Serine hydroxymethyltransferase, cytosolic 3.2~4.8 0.389 3 /5 SHMT1 P34896 7.61/54.5 191/40 35
Na(+)/H(+) exchange regulatory cofactor NHE-RF1 3.6~10.7 0.221 3 /5 SLC9A3R1 O14745 5.55/39.1 92/23 36
Glutamate dehydrogenase 1, mitochondrial 3.0~5.3 0.065 3 /5 GLUD1 P00367 7.66/62.6 60/24 34
Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial 2.6~15.6 0.246 3 /5 SUCLG2 Q96I99 6.15/47.8 116/26 34
Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial 2.6~5.4 <0.001* 5 /5 HADH Q16836 8.88/35.2 1089/45 48
Complement C3 2.5~3.1 0.737 3 /5 C3 P01024 6.02/192.2 2313/172 40
Alpha-crystallin B chain 2.7~4.1 0.560 3 /5 CRYAB P02511 6.76/20.4 4522/602 72
Acetyl-CoA acetyltransferase, mitochondrial 2.4~4.0 0.946 3 /5 ACAT1 P24752 8.98/46.4 670/64 55
Carbonic anhydrase 2 2.4~74.2 0.889 3 /5 CA2 P00918 6.87/30.0 229/51 34
60 kDa heat shock protein, mitochondrial 2.4~5.5 0.073 3 /5 HSPD1 P10809 5.70/62.7 12507/ 660 65
Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial 2.3~4.9 <0.001* 4 /5 ECH1 Q13011 8.16/36.68 279/13 35
Cytochrome b5 2.3~9.9 0.637 3 /5 CYB5A P00167 4.88/15.5 392/21 55
ATP synthase subunit beta, mitochondrial 2.3~3.3 0.169 3 /5 ATP5B P06576 5.26/57.2 1348/130 63
Guanine deaminase 2.2~5.3 0.659 3 /5 GDA Q9Y2T3 5.44/51.4 47/24 35
Thioredoxin-dependent peroxide reductase, mitochondrial 2.3~6.3 0.996 3 /5 PRDX3 P30048 7.67/28.4 256/21 42
Quinone oxidoreductase 2.1~7.7 <0.001* 5 /5 CRYZ Q08257 8.56/36.0 495/36 41
UDP-glucuronosyltransferase 2B7 2~14.0 0.426 3 /5 UGT2B7 P16662 8.54/62.2 77/22 33
Electron transfer flavoprotein subunit beta 2.0~4.4 0.015 3 /5 ETFB P38117 8.24/28.8 34/21 30
Electron transfer flavoprotein subunit alpha, mitochondrial 2.2~10.4 0.020 3 /5 ETFA P13804 8.62/115.9 1110/50 45
L-lactate dehydrogenase B chain 2.1~8.7 0.006 3 /5 LDHB P07195 5.71/37.6 672/68 63
D = Deuterium labeling (RCC tissues); H = Hydrogen labeling (normal tissues)
Statistically significant data by student t-test
Table 2: Down-regulated proteins (D/H ratio ≤ 0.5) were displayed in at least three of five renal clear cell carcinoma (RCC) tissues analyzed by nanoLC-MS/MS coupled with stable isotope dimethyl labeling.