Table 2– Proteins specifically recognised by serum immunoglobulin G from patients with systemic sclerosis and pulmonary artery hypertension, identified by mass spectrometry (MS)

Protein ID on gel	Protein	SwissProt accession number	Theoretical/estimated molecular weight kDa	Theoretical/estimated pI	MS
Protein ID on gel	Protein	SwissProt accession number	Theoretical/estimated molecular weight kDa	Theoretical/estimated pI	Number of unique identified peptides^#	Total ion score	Best ion score	Sequence coverage %
234	Vinculin	VINC_HUMAN	124/114	5.5/6.4	15/23	739	108	28
312	Endoplasmin	ENPL_HUMAN	92/100	4.8/5.3	11/22	311	58	32
317	Splicing factor, proline- and glutamine-rich	SFPQ_HUMAN	76/100	9.5/6.7	4/7	95	50	13
365	Protein NOXP20	NXP20_HUMAN	61/96	4.6/4.8	4/12	92	57	34
486	TATA-binding protein-associated factor 2N	RBP56_HUMAN	62/76	8.0/9.0	2/4	66	39	9
494	TATA-binding protein-associated factor 2N	RBP56_HUMAN	62/76	8/9.3	2/5	57	44	15
575	Heat shock cognate 71-kDa protein	HSP7C_HUMAN	71/75	5.4/5.7	9/10	308	77	21
585	Heat shock cognate 71-kDa protein	HSP7C_HUMAN	71/74	5.4/5.3	2/3	50	29	6
586	Heat shock cognate 71-kDa protein	HSP7C_HUMAN	71/74	5.4/5.3	6/7	210	49	16
622	Heat shock cognate 71-kDa protein	HSP7C_HUMAN	71/72	5.4/5.7	5/13	88	37	24
645	Lamin-A/C	LMNA_HUMAN	74/70	6.6/6.5	9/26	223	49	38
671	Cytoskeleton-associated protein 4	CKAP4_HUMAN	66/67	5.6/5.2	3/6	80	32	12
732	Lamin-A/C	LMNA_HUMAN	74/62	6.6/7.5	3/18	88	39	25
835	ATP synthase subunit α, mitochondrial precursor	ATPA_HUMAN	60/55	9.2/8.5	4/7	109	41	15
860	Tubulin β chain	TBB5_HUMAN	50/53	4.8/5.3	9/16	379	88	48
942	NADPH:adrenodoxin oxidoreductase, mitochondrial precursor	ADRO_HUMAN	54/50	8.7/8.8	7/13	122	28	30
1001	Heterogeneous nuclear ribonucleoprotein D0	HNRPD_HUMAN	38/49	7.6/6.5	2/2	79	51	6
1015	Phosphoglycerate kinase 1	PGK1_HUMAN	45/49	8.3/9.1	10/16	437	71	46
1077	Calumenin precursor	CALU_HUMAN	37/45	4.5/4.4	6/10	148	32	41
1078	40S ribosomal protein SA	RSSA_HUMAN	33/45	4.8/5	8/10	433	125	51
1124	Fructose-bisphosphate aldolase A	ALDOA_HUMAN	39/42	8.3/9.8	7/12	273	90	46
1167	28S ribosomal protein S22, mitochondrial	RT22_HUMAN	41/40	7.7/6.9	5/7	73	28	20
1176	Heterogeneous nuclear ribonucleoproteins C1/C2	HNRPC_HUMAN	34/39	5/5.4	3/4	118	63	18
1195	Protein SET	SET_HUMAN	33/39	4.2/5.5	3/7	64	36	27
1213	60-kDa heat shock protein, mitochondrial	CH60_HUMAN	61/37	5.7/5.1	2/8	49	33	20
1217	N(G),N(G)-dimethylarginine dimethylaminohydrolase 1	DDAH1_HUMAN	31/37	5.5/6	5/9	212	72	36
1304	Heterogeneous nuclear ribonucleoproteins A2/B1	ROA2_HUMAN	37/36	9.0/9.0	7/8	320	83	30
1310	Elongation factor 1-delta	EF1D_HUMAN	31/36	4.9/5.2	4/7	53	21	35
1352	Voltage-dependent anion-selective channel protein 2	VDAC2_HUMAN	32/33	7.5/7.4	3/7	90	42	37
1412	Complement component 1 Q subcomponent-binding protein, mitochondrial precursor	C1QBP_HUMAN	31/30	4.7/4.5	6/7	471	113	48
1420	N(G),N(G)-dimethylarginine dimethylaminohydrolase 2	DDAH2_HUMAN	30/30	5.7/6.1	4/7	84	48	35
1429	Lysosomal protective protein precursor	PPGB_HUMAN	54/29	6.2/5.1	2/2	55	29	5
1470	Eukaryotic translation initiation factor 4H	IF4H_HUMAN	27/28	6.7/8.3	3/3	176	87	14
1473	Electron transfer flavoprotein subunit β	ETFB_HUMAN	28/28	8.2/9.5	5/8	120	49	40
1502	14-3-3 protein β/α	1433B_HUMAN	28/27	4.8/5.1	3/5	191	103	28
1526	Proteasome subunit α type-5	PSA5_HUMAN	26/26	4.7/5	6/8	160	70	41
1589	Ubiquitin carboxyl-terminal hydrolase isozyme L1	UCHL1_HUMAN	25/25	5.3/5.6	5/6	219	72	38
1612	Flavin reductase	BLVRB_HUMAN	22/25	7.1/8.6	4/8	82	24	65
1620	Peroxiredoxin-1	PRDX1_HUMAN	22/25	8.3/8.8	6/7	202	60	37
1633	Peroxiredoxin-2	PRDX2_HUMAN	22/23	5.7/6	6/10	367	95	50
1708	Myosin regulatory light chain 2, nonsarcomeric	MLRM_HUMAN	20/19	4.7/4.9	6/7	377	102	52
1753	Actin-related protein 2/3 complex subunit 5	ARPC5_HUMAN	16/17	5.5/6.1	6/6	426	102	52
2086	S-formylglutathione hydrolase	ESTD_HUMAN	31/32	6.5/7.3	4/9	150	73	52

pI: isoelectric point; ATP: adenosine triphosphate; NADPH: reduced nicotinamide adenosine dinucleotide. ^#: number of unique identified peptides with MS/MS and MS+MS/MS searches.