Supplementary Table and Figures

Analytical and Bioanalytical Chemistry

Electronic Supplementary Material

Identification of human hepatocellular carcinoma-related proteins by proteomic approaches

Ming-Hui Yang, Yu-Chang Tyan, Shiang-Bin Jong, Ying-Fong Huang, Pao-Chi Liao, Ming-Chen Wang

Table S1 – The 29 serum proteins identified with higher confidence levels (at least two unique peptide sequences matched) by nano-HPLC-ESI-MS/MS in this study.

NCBI Accession No. / Protein name a / Peptide sequence b
4502027 / albumin precursor / K.AEFAEVSKLVTDLTK.V
K.DLGEENFK.A
K.FQNALLVR.Y
K.KLVAASQAALGL
K.KQTALVELVK.H
K.KVPQVSTPTLVEVSR.N
K.LVAASQAALGL
K.LVNEVTEFAK.T
K.QTALVELVK.H
K.VPQVSTPTLVEVSR.N
R.AFKAWAVAR.L
R.FKDLGEENFK.A
R.QIKKQTALVELVK.H
4502109 / annexin VI isoform 1 @ / K.AM#KGLGTRDNTLIR.I
R.QRQEVCQSYK.S
4502149 / apolipoprotein A-II precursor / K.SKEQLTPLIK.K
K.SKEQLTPLIKK.A
K.VKSPELQAEAK.S
4502151 / apolipoprotein A-IV precursor / K.ALVQQMEQLR.T
K.LGEVNTYAGDLQK.K
K.LNHQLEGLTFQMK.K
R.DKVNSFFSTFK.E
R.ENADSLQASLRPHADELK.A
4502153 / apolipoprotein B precursor / K.AVSM#PSFSILGSDVR.V
K.AVSMPSFSILGSDVR.V
K.LLSGGNTLHLVSTTK.T
K.STSPPKQAEAVLK.T
K.SVSLPSLDPASAK.I
K.TEVIPPLIENR.Q
K.VNWEEEAASGLLTSLK.D
R.NLQNNAEWVYQGAIR.Q
R.TSSFALNLPTLPEVK.F
4502501 / complement component 4B proprotein / K.TEQWSTLPPETK.D
K.VLSLAQEQVGGSPEK.L
R.GLEEELQFSLGSK.I
4502511 / complement component 9 @ / K.LSPIYNLVPVK.M
R.SIEVFGQFNGKR.C
4504349 / hemoglobin beta chain / K.EFTPPVQAAYQK.V
K.SAVTALWGK.V
K.VLGAFSDGLAHLDNLK.G
K.VNVDEVGGEALGR.L
K.VVAGVANALAHK.Y
K.VVAGVANALAHKYH
4504783 / inter-alpha (globulin) inhibitor H2 / K.AHVSFKPTVAQQR.I
K.FYNQVSTPLLR.N
K.IQPSGGTNINEALLR.A
K.VQFELHYQEVK.W
4507725 / transthyretin / K.AADDTWEPFASGK.T
R.GSPAINVAVHVFR.K
4557225 / alpha-2-macroglobulin precursor / K.AAQVTIQSSGTFSSK.F
K.AIGYLNTGYQR.Q
K.SKAIGYLNTGYQR.Q
R.SASNMAIVDVK.M
4557321 / apolipoprotein A-I precursor / K.ATEHLSTLSEK.A
K.DLATVYVDVLK.D
K.DLATVYVDVLKDSGR.D
K.DSGRDYVSQFEGSALGK.Q
K.LLDNWDSVTSTFSK.L
K.VEPLRAELQEGAR.Q
K.VQPYLDDFQKK.W
K.VSFLSALEEYTK.K
R.DYVSQFEGSALGK.Q
R.EQLGPVTQEFWDNLEK.E
R.LEALKENGGAR.L
R.QGLLPVLESFK.V
R.VKDLATVYVDVLK.D
4557323 / apolipoprotein C-III precursor / K.DALSSVQESQVAQQAR.G
R.GWVTDGFSSLK.D
4557325 / apolipoprotein E precursor / K.VQAAVGTSAAPVPSDNH
R.AATVGSLAGQPLQER.A
R.GEVQAMLGQSTEELR.V
4557385 / complement component 3 precursor / K.AGDFLEANYMNLQR.S
K.DFDFVPPVVR.W
K.ENEGFTVTAEGK.G
K.GQGTLSVVTMYHAK.A
K.SSLSVPYVIVPLK.T
R.SGIPIVTSPYQIHFTK.T
R.TVMVNIENPEGIPVK.Q
4557485 / ceruloplasmin (ferroxidase) @ / K.GAYPLSIEPIGVR.F
K.NNEGTYYSPNYNPQSR.S
4557871 / transferrin / K.EGYYGYTGAFR.C
K.GDVAFVKHQTVPQNTGGK.N
K.HQTVPQNTGGKNPDPWAK.N
K.SASDLTWDNLK.G
K.SASDLTWDNLKGK.K
K.YLGEEYVK.A
R.TAGWNIPMGLLYNK.I
4826762 / haptoglobin / K.LRTEGDGVYTLNNEK.Q
K.VTSIQDWVQK.T
K.VVLHPNYSQVDIGLIK.L
R.NANFKFTDHLK.Y
R.TEGDGVYTLNNEK.Q
R.VGYVSGWGR.N
9257232 / orosomucoid 1 precursor / K.NWGLSVYADKPETTK.E
K.SDVVYTDWKK.D
R.YVGGQEHFAHLLILR.D
10835095 / serum amyloid A4 @ / R.AYWDIMISNHQNSNR.Y
R.GPGGVWAAK.L
11321561 / hemopexin / K.GGYTLVSGYPK.R
K.NFPSPVDAAFR.Q
K.SGAQATWTELPWPHEK.V
K.VWVYPPEKK.E
R.EWFWDLATGTMK.E
R.LWWLDLK.S
R.RLWWLDLK.S
R.WKNFPSPVDAAFR.Q
13540475 / serum amyloid A2 @ / K.RGPGGAWAAEVISNAR.E
R.EANYIGSDKYFHAR.G
R.GPGGAWAAEVISNAR.E
21071030 / alpha 1B-glycoprotein / K.NGVAQEPVHLDSPAIK.H
R.ATWSGAVLAGR.D
R.SGLSTGWTQLSK.L
21361198 / serine (or cysteine) proteinase inhibitor / K.AVHKAVLTIDEK.G
K.DTEEEDFHVDQVTTVK.V
K.GKWERPFEVK.D
K.LQHLENELTHDIITK.F
K.SVLGQLGITK.V
K.VFSNGADLSGVTEEAPLK.L
38044288 / gelsolin isoform b / K.AGALNSNDAFVLK.T
K.QTQVSVLPEGGETPLFK.Q
40316910 / serum amyloid A1 isoform 2 @ / K.RGPGGAWAAEVISDAR.E
R.GPGGAWAAEVISDAR.E
42716297 / clusterin isoform 1 / K.LFDSDPITVTVPVEVSR.K
K.YVNKEIQNAVNGVK.Q
45580723 / haptoglobin-related protein / K.DIAPTLTLYVGKK.Q
K.GSFPWQAK.M
R.ILGGHLDAK.G
R.LRTEGDGVYTLNDKK.Q
R.TEGDGVYTLNDKK.Q
51472914 / Immunoglobulin domain variable region ^ / R.GDEPTSPSTDLQAK.H
R.NLPGGC*VLGAAAGK.S

a) @: Proteins were only in HCC patient group. ^: Immunoglobulin domain variable region was only in normal individual group.

b) The amino acid modifications: #: Oxidation on methionine, average mass change: 15.9994; *: Carboxyamidomethylation on cysteine, average mass change: 57.0215 in the database searching by SEQUEST.

(a)

(b)

(c)

Fig. S1 – MS/MS spectral data of three peptides from the HCC patients’ serum sample. (a) C-reactive protein precursor, peptide GYSIFSYATK (M/Z = 569.2, +2), (b) Ig gamma-1 chain C region, peptide FNWYVDGVEVHNAK (M/Z = 560.2, +3), (c) Complement factor B precursor, peptide YGLVTYATYPK (M/Z = 638.3, 2+). Interpretation of the complete y-ion and b-ion series provides the peptide sequences as shown.

(a)

(b)

Fig.S2 – MS/MS spectra of two peptides from the analysis of HCC patient’s serum that was derived from serum amyloid A2 (a), and ceruloplasmin (b). The spectra showed the fragmentation patterns of a doubly charged precursor ion at m/z 835.2, and 685.5. Interpretation of the complete y-ion and b-ion series provides the peptide sequences REANYIGSDKYFHARG, and KGAYPLSIEPIGVRF as shown.