Table 1. Identified proteins by MS/MS analysis.

Spot no.	Protein description	Gene name	Function	Accession no.	Theoretical Mr/pIa	Score	No. of pepb	Fold changec,d,e
1	Peptidyl-prolyl cis-trans isomerase A	PPIA	Metabolism	P62937	17 881/7.82	198	22	↑2.3±0.5
2	Ubiquitin-conjugating enzyme E2 N	UBE2N	Proteolysis	P61088	17 184/6.13	91	2	↓3.2±0.7
3	Triosephosphate isomerase	TPI1	Metabolism	P60174	26 538/6.51	634	17	↑2.9±0.4
4	Hypoxia-inducible factor 1-alpha	HIF1A	Metabolism	Q16665	92 670/5.17	145	12	↑NA
5	Nucleoside diphosphate kinase B	NME2	Apoptosis regulation	P22392	17 298/8.55	45	1	↓2.0±0.2
6	Peroxiredoxin-5	PRDX5	Apoptosis regulation	P30044	17 030/6.73	320	17	↑NA
7	Low-molecular-weight phosphotyrosine protein phosphatase	ACP1	Metabolism	P24666	17 911/6.35	117	8	↑NA
8	Peroxiredoxin-2	PRDX2	Apoptosis regulation	P32119	17 660/6.84	84	4	↑NA
9	Prefoldin subunit 2	PFDN2	Molecular chaperone	Q9UHV9	16 695/6.20	161	6	↓3.7±0.9
10	Programmed cell death protein 5	PDCD5	Apoptosis regulation	Q2HJH9	14 094/6.21	123	3	↓2.9±0.6
11	Cytochrome c oxidase subunit 5A, mitochondrial	COX5A	Metabolism	P20674	16 935/6.30	69	1	↑2.1±0.4
12	Galectin-7	LGALS7	Cell proliferation/differentiation	P47929	15 123/7.03	437	13	↓2.3±0.5
13	Pyruvate kinase isozymes M1/M2	PKM2	Metabolism	P14618	57 805/7.95	213	10	↑3.3±0.7
14	Proteasome subunit beta type-2	PSMB2	Proteolysis	P49721	22 836/6.52	436	36	↑2.5±0.3
15	Proteasome subunit beta type-4	PSMB4	Proteolysis	P28070	25 204/5.47	428	15	↑4.3±1.4
16	Superoxide dismutase (Cu-Zn)	SOD1	Electron transport/redox regulation	P00441	15 804/5.70	64	6	↑2.2±0.8
17	Splicing factor, arginine/serine-rich 7	SFRS7	mRNA splicing	Q16629	27 578/11.83	134	5	↓3.9±1.1
18	3-Hydroxyacyl-CoA dehydrogenase type-2	HSD17B10	Metabolism	Q99714	27 134/7.66	298	6	↓2.0±0.5
19	Superoxide dismutase (Mn)	SOD2	Electron transport/redox regulation	P04179	24 722/8.35	52	3	↓2.1±0.3
20	Malate dehydrogenase, cytoplasmic	MDH1	Metabolism	P40925	36 426/6.89	391	9	↓2.3±0.6
21	Eukaryotic translation initiation factor 4H	EIF4H	Transcription regulation	Q15056	27 425/6.67	276	8	↓5.3±1.8
22	28-kDa Heat- and acid-stable phosphoprotein	PDAP1	Cell proliferation/differentiation	Q13442	20 630/8.84	153	7	↑2.3±1.1
23	Phosphatidylethanolamine-binding protein	PEBP1	Signal transduction	P30086	21 057/7.01	106	3	↓2.0±0.4
24	26S proteasome non-ATPase regulatory subunit 8	PSMD8	Proteolysis	P48556	30 005/6.85	121	12	↑2.4±0.9
25	Myosin regulatory light polypeptide 9	MYL9	Calcium ion binding	P24844	19 695/4.80	68	3	↑2.0±0.2
26	Ig kappa chain C region	IGKC	Immune response	P01834	11 773/5.58	378	11	↑3.4±0.7
27	Chromobox protein homolog 3	CBX3	Transcription regulation	Q13185	20 811/5.23	256	8	↑NA
28	Heat shock protein beta-1	HSPB1	Molecular chaperone	P04792	22 783/5.98	188	15	↑2.0±0.6
29	Rho GDP-dissociation inhibitor 2	ARHGDIB	Signal transduction	P52566	22 988/5.1	68	7	↑2.1±1.3
30	Charged multivesicular body protein 4b	CHMP4B	Protein binding	Q9H444	24 950/4.76	268	9	↑2.4±0.8
31	Inorganic pyrophosphatase	PPA1	Metabolism	Q15181	32 660/5.54	106	6	↑2.3±0.5
32	Heterogeneousnuclear ribonucleoprotein H3	HNRPH3	mRNA splicing	P31942	36 960/6.37	134	4	↓2.7±0.6
33	NADH dehydrogenase flavoprotein 2	NDUFV2	Electron transport/redox regulation	P19404	27 392/5.22	241	7	↓NA
34	LIM and SH3 domain protein 1	LASP1	Zinc ion binding	Q14847	30 097/6.61	100	4	↑2.3±0.5
35	Tumor-suppressor candidate 2	TUSC2	Protein binding	O75896	11 942/9.69	36	2	↓2.0±0.7
36	Alcohol dehydrogenase (NADP)	AKR1A1	Metabolism	P14550	36 892/6.32	421	29	↑2.0±0.9
37	Annexin A5	ANXA5	Calcium ion binding	P08758	35 937/4.94	217	6	↑3.6±1.5
38	Cytochrome b-c1 complex subunit 1, mitochondrial	UQCRC1	Metabolism	P31930	52 646/5.43	423	24	↓2.9±1.2
39	Creatine kinase M-type	CKM	Metabolism	P06732	43 302/6.77	708	21	↑5.2±1.4
40	UDP-glucose 4-epimerase	GALE	Metabolism	Q14376	38 656/6.26	152	7	↓2.1±0.4
41	L-lactate dehydrogenase A chain	LDHA	Metabolism	P00338	36 689/8.46	467	14	↑2.9±0.8
42	Fructose-bisphosphate aldolase C	ALDOC	Metabolism	P09972	39 324/6.46	413	5	↑2.0±0.4

All protein spots identified by ESI-Q-TOF MS/MS as significantly changed in average expression level in Hela-R cells compared with parental Hela cells

^aTheoretical Mr/pI: theoretical molecular weight (kDa) and pI from the ExPASy database

^bNo. of pep: number of unique peptides identified by MS/MS sequencing

^cUpward arrows: upregulated

^dDownward arrows: downregulated

^eNA: the spots on one of the paired gels were too weak or nondetectable