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. Author manuscript; available in PMC: 2013 Jun 3.
Published in final edited form as: J Proteome Res. 2010 Mar 5;9(3):1402–1415. doi: 10.1021/pr900932y

Table 1.

Identified H2AX-interacting Proteins in HCC QGY7703 Cells.

IPI no. Gene symbol Protein namea No.of peptide-matched Enrichment-foldb S.D.
IPI00219037.5 H2AX Histone H2AX (bait) 4 9.11
Apoptosis
IPI00012011.6 CFL1 Cofilin-1 2 1.90 0.014
IPI00291262.3 CLU Clusterin precursor 2 2.26 0.56
IPI00027230.3 HSP90B1 Endoplasmin precursor 8 1.60 0.07
IPI00304925.4 HSPA1A Heat shock 70 kDa protein 1 3 1.50 0.16
IPI00555692.2 ANXA4 ANXA4 protein 2 1.49 0.72
IPI00329801.12 ANXA5 Annexin A5 6 1.36 0.11
IPI00025277.5 PDCD6 Programmed cell death protein 6 3 1.745 0.19
IPI00171438.2 TXNDC Thioredoxin domain-containing protein 5 precursor 2 1.62 0.08
IPI00291467.7 SLC25A6 ADP/ATP translocase 3 2 1.72 0.057
Response to protein stimulus, oxidative stress and hypoxia
IPI00023137.1 TOR1B Torsin B precursor 2 2.71 0.70
IPI00382470.3 HSP90AA1 Heat shock protein HSP 90-alpha 2 3 2.57 0.19
IPI00301277.1 HSPA1L Heat shock 70 kDa protein 1L 3 1.45 0.13
IPI00030275.5 TRAP1 Heat shock protein 75 kDa mitochondrial precursor 9 2.45 0.24
IPI00220301.5 PRDX6 Peroxiredoxin-6 3 1.73 0.38
IPI00027192.5 PLOD1 Procollagen-lysine,2-oxoglutarate 5-dioxygenase precursor 2 2.46 0.03
IPI00022314.1 SOD2 Superoxide dismutase90, 2 2.56 0.22
DNA repair (14)
IPI00000690.1 AIFM1 Isoform 1 of Apoptosis-inducing factor 1, mitochondrial precursor 6 2.93 0.37
IPI00304596.3 NONO Non-POU domain-containing octamer-binding protein 2 1.93 0.02
IPI00449049.5 PARP1 Poly [ADP-ribose] polymerase 1 2 1.81 0.07
IPI00020599.1 CALR Calreticulin precursor 7 1.34 0.20
IPI00021263.3 YWHAZ 14-3-3 protein zeta/delta 3 1.37 0.11
IPI00000816.1 YWHAE 14-3-3 protein epsilon 3 1.71 0.10
IPI00413293.5 TOR1A Torsin A precursor 2 1.81 0.56
IPI00000877.1 HYOU1 150 kDa oxygen-regulated protein precursor 4 2.68 0.28
IPI00029744.1 SSBP1 Single-stranded DNA-binding protein, mitochondrial precursor 2 1.74 1.12
IPI00169383.3 PGK1 Phosphoglycerate kinase 1 4 2.58 0.61
IPI00219365.3 MSN Moesin 2 1.96 0.76
IPI00025491.1 EIF4A1 Eukaryotic initiation factor 4A-I 2 1.41 0.04
IPI00008438.1 RPS10 40S ribosomal protein S10 2 2.14 0.03
IPI00011062.1 CPS1 Isoform 1 of Carbamoyl-phosphate synthase [ammonia], mitochondrial precursor 4 1.44 0.05
DNA metabolism
IPI00005198.2 ILF2 Interleukin enhancer-binding factor 2 3 1.71 0.12
IPI00453473.6 HIST2H4A Histone H4 5 2.27 0.44
Ca2+ binding signaling (6)
IPI00418169.3 ANXA2 annexin A2 isoform 1 3 1.67 0.27
IPI00334627.3 ANXA2P2 Similar to annexin A2 isoform 1 6 1.84 0.20
IPI00075248.11 CALM2 Calmodulin 6 5.35 0.97
IPI00032313.1 S100A4 Protein S100-A4 2 1.87 0.01
IPI00018235.3 PEF1 Peflin 2 3.08 0.54
IPI00002459.4 ANXA6 annexin VI isoform 2 8 2.19 0.22
Cell cycle
IPI00216318.5 YWHAB tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide 2 1.48 0.04
IPI00017297.1 MATR3 Matrin-3 2 2.44 0.02
Alcohol metabolic process
IPI00465439.5 ALDOA Fructose-bisphosphate aldolase A 2 2.015 0.049
IPI00220644.8 PKM2 pyruvate kinase 3 isoform 2 6 2.45 0.27
IPI00479186.5 PKM2 pyruvate kinase 3 isoform 1 2 2.34 0.17
IPI00465248.5 ENO1 enolase 1 2 1.945 0.16
IPI00058192.1 POFUT1 Isoform 1 of GDP-fucose protein O-fucosyltransferase 1 precursor 3 1.86 0.05
IPI00219217.3 LDHB L-lactate dehydrogenase B chain 2 2.15 0.19
RNA metabolism
IPI00301936.3 ELAVL1 ELAV-like protein 1 3 1.47 0.22
IPI00028888.1 HNRPD Isoform 1 of Heterogeneous nuclear ribonucleoprotein D0 3 1.39 0.49
IPI00011274.2 HNRPDL heterogeneous nuclear ribonucleo protein D-like 2 1.84 0.10
IPI00013877.2 HNRPH3 Isoform 1 of Heterogeneous nuclear ribonucleoprotein H3 2 3.12 0.36
IPI00012074.3 HNRPR Heterogeneous nuclear ribonucleoprotein R 5 3.26 0.31
IPI00106509.2 HNRPAB Isoform 4 of Heterogeneous nuclear ribonucleoprotein A/B 2 4.57 0.13
IPI00012066.2 PCBP2 poly(rC)-binding protein 2 isoform b 2 1.86 0.77
IPI00008524.1 PABPC1 Isoform 1 of Polyadenylate-binding protein 1 2 4.18 0.54
IPI00221035.3 BTF3 Isoform 1 of Transcription factor BTF3 2 2.63 0.05
IPI00073713.3 MSI2 Isoform 1 of RNA-binding protein Musashi homolog 2 2 2.81 0.65
IPI00328840.9 THOC4 THO complex subunit 4 3 4.76 0.70
IPI00018140.3 SYNCRIP Isoform 1 of Heterogeneous nuclear ribonucleoprotein Q 9 2.62 0.35
IPI00215965.2 HNRPA1 heterogeneous nuclear ribonucleoprotein A1 isoform b 2 1.42 0.20
IPI00386854.5 HNRPA2B1 HNRPA2B1 protein 4 2.59 0.17
IPI00216592.2 HNRPC Isoform C1 of Heterogeneous nuclear ribonucleoproteinsC1/C2 3 1.84 0.04
Establishment of cellular localization
IPI00018931.6 VPS35 Vacuolar protein sorting-associated protein35 3 1.845 0.15
IPI00024911.1 ERP29 Endoplasmic reticulum protein ERp29 precursor 5 1.49 0.16
IPI00156689.3 VAT1 Synaptic vesicle membrane protein VAT-1 homolog 3 2.27 0.45
IPI00021405.3 LMNA Isoform A of Lamin-A/C 3 1.53 0.06
IPI00045839.3 LEPRE1 Isoform 3 of Prolyl 3-hydroxylase 1 precursor 3 1.35 0.15
IPI00009904.1 PDIA4 Protein disulfide-isomerase A4 precursor 11 1.58 0.08
IPI00020436.4 RAB11B Ras-related protein Rab-11B 3 1.47 0.60
IPI00023748.3 NACA Nascent polypeptide-associated complex subunit alpha 2 1.50 0.63
Cellular macromolecule metabolism
IPI00021728.3 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 2 1.36 0.13
IPI00178440.3 EEF1B2 Elongation factor 1-beta 2 1.52 0.58
IPI00299571.5 PDIA6 Isoform 2 of Protein disulfide-isomerase A6 precursor 9 1.60 0.05
IPI00010720.1 CCT5 T-complex protein 1 subunit epsilon 2 1.57 012
IPI00011229.1 CTSD Cathepsin D precursor 3 3.61 0.39
IPI00386755.2 ERO1L ERO1-like protein alpha precursor 2 1.56 0.11
IPI00010796.1 P4HB Protein disulfide-isomerase precursor 6 1.47 0.42
IPI00011937.1 PRDX4 Peroxiredoxin-4 3 2.19 0.27
IPI00419585.9 PPIA Peptidyl-prolyl cistrans isomerase A 4 1.44 0.06
IPI00028004.2 PSMB3 Proteasome subunit beta type 3 2 2.26 0.74
IPI00008529.1 RPLP2 60S acidic ribosomal protein P2 2 1.40 0.01
IPI00555956.2 PSMB4 Proteasome subunit beta type 4 precursor 2 1.76 0.43
IPI00303300.3 FKBP10 FK506-binding protein 10 precursor 3 2.39 0.96
IPI00171412.1 SUMF2 Isoform 1 of Sulfatase-modifying factor 2 precursor 2 2.38 0.02
IPI00003128.1 P4HA2 Isoform IIb of Prolyl 4-hydroxylase subunit alpha-2 precursor 3 2.3 0.14
IPI00028635.4 RPN2 Dolichyl-diphosphooligosaccharide—protein glycosyltransferase 63 kDa subunit precursor 7 2.20 0.02
Cell redox homeostasis
IPI00026328.3 TXNDC12 Thioredoxin domain-containing protein 12 precursor 3 1.35 0.04
IPI00303568.3 PTGES2 Prostaglandin E synthase 2 6 1.71 0.34
Carboxylic acid metabolism
IPI00017726.1 HSD17B10 hydroxysteroid (17-beta) dehydrogenase 10isoform 1 5 2.15 0.35
IPI00643920.2 TKT Transketolase 3 3.52 0.31
Carbohydrate catabolism
IPI00011454.1 GANAB Isoform 2 of Neutral alpha-glucosidase AB precursor 3 1.44 0.42
IPI00441344.1 GLB1 Beta-galactosidase precursor 2 4.08 0.38
IPI00383046.3 CMBL carboxymethylenebutenolidase-like 7 4.15 0.29
IPI00026154.2 PRKCSH Glucosidase 2 subunit beta precursor 4 2.21 1.00
IPI00023673.1 LGALS3BP Galectin-3-binding protein Precursor 3 3.22 0.29
IPI00027851.1 HEXA Beta-hexosaminidase alpha chain Precursor 2 3.01 0.16
Others
IPI00020075.4 ABHD10 CDNA FLJ11342 fis, clone PLACE1010800 3 2.10 0.05
IPI00168479.2 APOA1BP apolipoprotein A-I binding protein precursor 3 3.36 0.22
IPI00550363.3 CCDC19 Transgelin-2 3 1.44 0.67
IPI00329696.1 FAM82B Protein FAM82B 3 3.08 0.08
IPI00007765.5 HSPA9 Stress-70 protein, mitochondrial precursor 9 1.63 0.74
IPI00024919.3 PRDX3 Thioredoxin-dependent peroxide reductase, mitochondrial precursor 3 2.81 0.34
IPI00377161.7 HIBCH 3-hydroxyisobutyryl-Coenzyme A hydrolase isoform 2 2 4.32 0.63
a

Only the proteins with two or more peptides matched are listed.

b

Fold of enrichment was calculated as the ratio of Leu-d3-labeled peptide to unlabeled peptide.