Mass spectrometry-based analysis of formalin-fixed, paraffin-embedded distal cholangiocarcinoma identifies stromal thrombospondin-2 as a potential prognostic marker

Byrling, Johannes; Kristl, Theresa; Hu, Dingyuan; Pla, Indira; Sanchez, Aniel; Sasor, Agata; Andersson, Roland; Marko-Varga, György; Andersson, Bodil

doi:10.1186/s12967-020-02498-3

Table 2 Proteins found to be differentially expressed in the PRM analysis (q < 0.05, FC ≥ 2 or ≤ 0.5) between the distal cholangiocarcinoma samples and controls

From: Mass spectrometry-based analysis of formalin-fixed, paraffin-embedded distal cholangiocarcinoma identifies stromal thrombospondin-2 as a potential prognostic marker

#	Accession	Gene	Protein Name	Peptide Sequence	Values Cancer	Values Control	q-value	FC Ca/Co	Literature CCA
A
1	P35442	TSP2	Thrombospondin-2	LVFNPDQEDLDGDGR	16	9	< 0.0001	29.3
2	P35442	TSP2	Thrombospondin-2	FDYIPPVNADDLSK	16	6	< 0.0001	8.3
3	Q6UX06	OLFM4	Olfactomedin-4	LLEYYR	16	8	< 0.0001	7.8	[71, 72]
4	P25815	S100P	Protein S100-P	YSGSEGSTQTLTK	16	9	< 0.0001	7.3	[63, 64]
5	P40199	CEAM6	Carcinoembryonic antigen-related cell adhesion molecule 6	IGYSWYK	16	9	0.0007	7.2	[65]
6	P25815	S100P	Protein S100-P	ELPGFLQSGK	16	8	< 0.0001	6.4	[63, 64]
7	Q04695	K1C17	Keratin, type I cytoskeletal 17	ASLEGNLAETENR	16	9	0.0044	5.5	[66, 67]
8	Q99439	CNN2	Calponin-2	GLQSGVDIGVK	16	8	< 0.0001	4.8
9	Q96CG8	CTHR1	Collagen triple helix repeat-containing protein 1	VLFSGSLR	16	9	< 0.0001	4.5
10	P08238	HS90B	Heat shock protein HSP 90-beta	NPDDITQEEYGEFYK	16	9	< 0.0001	4.2	[70]
11	P19971	TYPH	Thymidine phosphorylase	MLAAQGVDPGLAR	16	9	< 0.0001	4.1	[68, 69]
12	P31949	S10AB	Protein S100-A11	DGYNYTLSK	16	9	< 0.0001	3.8	[96]
13	P19971	TYPH	Thymidine phosphorylase	VAAALDDGSALGR	16	9	< 0.0001	3.6	[68, 69]
14	P19827	ITIH1	Inter-alpha-trypsin inhibitor heavy chain H1	AAISGENAGLVR	16	9	0.0030	3.5
15	Q96HE7	ERO1A	ERO1-like protein alpha	LGAVDESLSEETQK	16	9	< 0.0001	3.0
16	Q01518	CAP1	Adenylyl cyclase-associated protein 1	VENQENVSNLVIEDTELK	16	9	< 0.0001	2.9
17	Q9UBR2	CATZ	Cathepsin Z	NVDGVNYASITR	16	9	0.0004	2.7
18	P50454	SERPH	Serpin H1	AVLSAEQLR	16	9	< 0.0001	2.7	[97]
19	P21291	CSRP1	Cysteine and glycine-rich protein 1	GYGYGQGAGTLSTDK	16	9	0.0018	2.7
20	Q9UBR2	CATZ	Cathepsin Z	NSWGEPWGER	16	9	0.0007	2.6
21	P02792	FRIL	Ferritin light chain	ALFQDIK	16	9	0.0002	2.6
22	Q01518	CAP1	Adenylyl cyclase-associated protein 1	LSDLLAPISEQIK	16	9	< 0.0001	2.5
23	P42224	STAT1	Signal transducer and activator of transcription 1-alpha/beta	TELISVSEVHPSR	14	4	0.0033	2.5	[98]
24	Q9NZM1	MYOF	Myoferlin	ANVTVLDTQIR	16	6	0.0020	2.4
25	Q96CG8	CTHR1	Collagen triple helix repeat-containing protein 1	IIIEELPK	16	6	0.0020	2.4
26	P00338	LDHA	L-lactate dehydrogenase A chain	SADTLWGIQK	16	9	< 0.0001	2.4	[99, 100]
27	P00338	LDHA	L-lactate dehydrogenase A chain	VTLTSEEEAR	16	9	< 0.0001	2.3	[99, 100]
28	O75369	FLNB	Filamin-B	FNDEHIPESPYLVPVIAPSDDAR	16	9	0.0005	2.3
29	P43490	NAMPT	Nicotinamide phosphoribosyltransferase	STQAPLIIRPDSGNPLDTVLK	15	8	< 0.0001	2.2
30	Q9NZM1	MYOF	Myoferlin	GPVGTVSEAQLAR	16	9	< 0.0001	2.2
31	P40121	CAPG	Macrophage-capping protein	ANAQAAALYK	16	9	0.0006	2.2	[87]
32	P38606	VATA	V-type proton ATPase catalytic subunit A	TVISQSLSK	16	9	< 0.0001	2.2
33	P14618	KPYM	Pyruvate kinase PKM	LDIDSPPITAR	16	9	< 0.0001	2.1	[101]
34	P08238	HS90B	Heat shock protein HSP 90-beta	ALLFIPR	14	5	0.0021	2.1	[70]
35	P27348	1433 T	14–3-3 protein theta	YLIANATNPESK	16	9	0.0078	2.1	[102, 103]
36	P07900	HS90A	Heat shock protein HSP 90-alpha	NPDDITNEEYGEFYK	16	9	0.0092	2.1	[70]
37	P43490	NAMPT	Nicotinamide phosphoribosyltransferase	AVPEGFVIPR	16	7	< 0.0001	2.1
38	P14618	KPYM	Pyruvate kinase PKM	GDLGIEIPAEK	16	9	< 0.0001	2.1	[101]
39	P10809	CH60	60 kDa heat shock protein, mitochondrial	LVQDVANNTNEEAGDGTTTATVLAR	16	9	0.0408	2.0	[104]
B
1	P00352	AL1A1	Retinal dehydrogenase 1	TIPIDGNFFTYTR	16	9	0.0457	0.46	[105]
2	P04040	CATA	Catalase	ADVLTTGAGNPVGDK	16	9	< 0.0001	0.34	[106]
3	P04040	CATA	Catalase	FNTANDDNVTQVR	16	9	< 0.0001	0.32	[106]
4	P09525	ANXA4	Annexin A4	GLGTDDNTLIR	16	9	0.0005	0.32	[83]
5	Q16853	AOC3	Membrane primary amine oxidase	YQLAVTQR	16	9	< 0.0001	0.29
6	O95994	AGR2	Anterior gradientprotein 2 homolog	LPQTLSR	16	9	< 0.0001	0.29	[107]
7	O60218	AK1BA	Aldo–keto reductase family 1-member B10	SGDDLFPK	16	9	0.0152	0.27	[83]
8	Q13228	SBP1	Methanethiol oxidase	IYVVDVGSEPR	16	9	< 0.0001	0.26	[83]
9	P00167	CYB5	Cytochrome b5	FLEEHPGGEEVLR	16	9	< 0.0001	0.25	[83]
10	Q13228	SBP1	Methanethiol oxidase	LVLPSLISSR	14	5	0.0004	0.24	[83]
11	P51884	LUM	Lumican	ISNIPDEYFK	16	9	< 0.0001	0.18
12	Q9UBX5	FBLN5	Fibulin-5	DQPFTILYR	16	9	< 0.0001	0.18	[52]
13	Q07507	DERM	Dermatopontin	YFESVLDR	16	9	< 0.0001	0.18	[55]
14	P51884	LUM	Lumican	ILGPLSYSK	16	9	< 0.0001	0.16
15	P55083	MFAP4	Microfibril-associated glycoprotein 4	GFYYSLK	16	9	< 0.0001	0.16	[59]
16	P07585	PGS2	Decorin	VSPGAFTPLVK	16	9	< 0.0001	0.16	[49]
17	P51888	PRELP	Prolargin	NQLEEVPSALPR	16	9	< 0.0001	0.15
18	Q07507	DERM	Dermatopontin	GATTTFSAVER	16	9	< 0.0001	0.14	[55]
19	P55083	MFAP4	Microfibril-associated glycoprotein 4	WTVFQK	14	5	< 0.0001	0.12	[59]
20	P00325	ADH1B	Alcohol dehydrogenase 1B	AAVLWEVK	14	5	< 0.0001	0.12
21	P07585	PGS2	Decorin	ASYSGVSLFSNPVQYWEIQPSTFR	16	9	< 0.0001	0.11	[49]
22	P08294	SODE	Extracellular superoxide dismutase	VTGVVLFR	14	5	< 0.0001	0.11
23	P23141	EST1	Liver carboxylesterase 1	FTPPQPAEPWSFVK	16	9	< 0.0001	0.08	[52, 83]
24	P20774	MIME	Mimecan	LTLFNAK	16	9	< 0.0001	0.07	[52]
25	P23141	EST1	Liver carboxylesterase 1	TVIGDHGDELFSVFGAPFLK	16	9	< 0.0001	0.06	[52, 83]
26	P20774	MIME	Mimecan	DFADIPNLR	16	9	< 0.0001	0.05	[52]

Proteins are ordered by descending FC. (A) upregulated proteins. (B) downregulated proteins
Ca Cancer, CCA cholangiocarcinoma, Co Control, FC Fold Change

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