The Application of a Three-Step Serum Proteome Analysis for the Discovery and Identification of Novel Biomarkers of Hepatocellular Carcinoma

Table 3

Upregulated proteins identified by LC-MS/MS in human HCC serum. Details are described in the experimental procedures.

Protein name	Theoretical mass	Experimental mass	Score	Coverage	Queries matched
Afamin precursor	69024	90000	563	23%	16
Alpha-1-antichymotrypsin	48606	95000	118	4%	2
Alpha-1-B-glycoprotein	51908	95000	88	5%	2
Alpha-1-microglobulin	16531	230000	99	15%	2
Alpha-2-macroglobulin	163175	170000	2465	34%	76
Angiotensinogen	53122	55000	705	29%	23
Antithrombin III	49008	62000	389	24%	9
Apolipoprotein A-IV	45307	43000	639	30%	12
Apolipoprotein B	187126	140000	332	4%	7
Apolipoprotein B-100	515077	140000	267	1%	5
Apolipoprotein E	36185	35000	832	44%	33
Beta-actin	41710	41000	226	17%	4
C1q	26442	33000	113	11%	2
C2 precursor	83214	97000	557	15%	14
C3	187046	180000	613	7%	11
C3b	103886	120000	2042	26%	63
C3c	187046	33000	206	2%	4
C3d	120000	187046	153	1%	3
C3, isoform CRA_a	70000	143619	1636	28%	64
C4A	192741	24000	456	5%	21
C4B	40737	41000	138	7%	2
C5	141723	120000	248	4%	6
C6	104776	120000	96	4%	2
C7	93449	95000	874	22%	27
C8-alpha subunit	65111	55000	109	3%	2
C8-beta propeptide	62008	70000	323	11%	7
C8-gamma polypeptide	22206	23000	352	40%	15
C9	60359	70000	496	14%	12
Complement receptor type 2 (Cr2)	112900	160000	160	2%	2
Component factor B	85450	50000	163	4%	3
Cr2-C3d complex	34437	35000	151	10%	3
Complement component (3b/4b) receptor 1	61415	160000	102	4%	2
Carbonic anhydrase I	28852	25000	195	18%	4
Carbonic anhydrase II	29200	33000	208	18%	4
Carboxypeptidase N Polypeptide 1 precursor	52253	45000	147	11%	3
Carboxypeptidase N precursor	60578	97000	330	11%	6
Cathepsin D preproprotein	44524	49000	103	6%	2
Cationic trypsinogen	160000	120901	66	—	2
CD14 protein precursor	40111	55000	365	21%	8
Ceruloplasmin	115398	140000	1520	27%	44
Clusterin	48772	39000	95	8%	2
C-type lectin domain family 3, member B	22552	25000	243	24%	6
Fibronectin precursor	256529	230000	176	2%	3
Galectin 3 binding protein	65289	90000	177	3%	3
Gelsolin	85644	95000	474	15%	11
Glutathione peroxidase 3 precursor	25489	26000	167	16%	4
Hemopexin precursor	51512	50000	104	4%	2
Heparin cofactor II	57034	110000	372	21%	8
Insulin-like growth factor binding protein	65994	95000	176	6%	3
Interalpha-trypsin inhibitor heavy chain H1	101339	230000	631	14%	23
Interalpha-trypsin inhibitor heavy chain H2	106370	230000	862	15%	28
ITI family heavy chain-related protein	103321	120000	348	9%	6
Kininogen 1	47853	120000	355	13%	7
Lactate dehydrogenase B	36615	35000	217	13%	4
Leucine-rich alpha-2-glycoprotein 1	38154	50000	301	15%	8
Lumican	38375	70000	320	21%	7
M130 antigen	160000	120901	66	1%	2
Multimerin 2	104352	20000	88	1%	2
Pancreatic carboxypeptidase A1 precursor	47111	41000	92	5%	2
Peptidoglycan recognition protein 2 precursor	67927	70000	96	7%	2
Pigment epithelial-differentiating factor (serpin-F1)	46313	48000	946	50%	22
Plasma protease (C1) inhibitor precursor	55147	90000	829	25%	43
Prepro-plasma carboxypeptidase B	48411	62000	100	6%	2
Preserum amyloid P component	25381	30000	362	26%	13
Prolidase	54348	55000	82	3%	2
Proteasome alpha 4 subunit isoform 1	29465	33000	85	8%	2
Sex-hormone-binding globulin	43768	45000	391	28%	10
Thyroxine-binding globulin precursor	46295	55000	135	6%	3
Trypsin inhibitor	106647	55000	174	5%	3
Vascular cell adhesion molecule 1 isoform	81224	97000	133	3%	2
Vitamin D binding protein	51183	55000	669	21%	17
Vitamin K-dependent protein S	75074	95000	106	3%	2
Vitronectin	54308	10000	90	2%	2