. 2017 Sep 7;167:46–59. doi: 10.1016/j.jprot.2017.08.007

Table 1.

Differentially expressed protein spots identified by MS.

Spot n.	Protein description	MetaCore name^a	UniProt ID/name^b	Mascot search results			Mean %V ± SD × 10^− 4^c				1-Way ANOVA p-value
Spot n.	Protein description	MetaCore name^a	UniProt ID/name^b	Score	N. of matched peptides	Sequence coverage (%)	Control	CRTAP	P3H1	PPIB	1-Way ANOVA p-value
Cytoskeletal and nuclear organization, and development
8	Caldesmon	Caldesmon	Q05682/CALD1	199	25/46	29	214 ± 203^§^d	664 ± 200^§¥#	120 ± 160^¥	241 ± 49^#	0.012326
9	Prelamin-A/C	Lamin A/C	P02545/LMNA	136	15/25	22	119 ± 68^$	–	20 ± 20^$	35 ± 10	0.012354
12	Serine/threonine-protein kinase PAK 2	PAK2	Q13177/PAK2	143	12/17	33	424 ± 97^⁎	228 ± 68	426 ± 127^&	113 ± 59^⁎&	0.007873
16	Fascin	Fascin	Q16658/FSCN1	214	21/48	47	380 ± 161	–	–	–	0.00067
20	Septin-11	Septin 11	Q9NVA2/SEP11	62	5/7	10	71 ± 69^$	–	462 ± 218^$	–	0.002164
25	Annexin A2	Annexin II	P07355/ANXA2	216	18/24	43	101 ± 145^⁎	–	–	402 ± 69^⁎	0.002210
27	Annexin A2	Annexin II	P07355/ANXA2	227	20/30	48	63 ± 18	–	–	86 ± 41	0.000326
34	Rho GDP-dissociation inhibitor 1	RhoGDI alpha	P52565/GDIR1	169	15/33	50	1437 ± 443^§	216 ± 58^§#¥	1822 ± 393^¥	1345 ± 94^#	0.000456
41	Ragulator complex protein LAMTOR3	MP1	Q9UHA4/LTOR3	152	7/8	66	52 ± 25	66 ± 18	41 ± 7^&	101 ± 5^&	0.029419
42	Protein S100-A4	MTS1 (S100A4)	P26447/S10A4	115	7/11	45	3909 ± 572^§	1234 ± 646^§¥	3774 ± 1387^¥	3155 ± 367	0.005465

Protein fate (synthesis, folding, proteolysis)
1	Hypoxia up-regulated protein 1	HYOU1	Q9Y4L1/HYOU1	255	35/63	42	561 ± 110^⁎§	187 ± 162^§	419 ± 71	186 ± 151^⁎	0.009483
17	Heterogeneous nuclear ribonucleoprotein H	hnRNP H1	P31943/HNRH1	156	13/21	37	428 ± 92^§	1155 ± 96^§¥#	175 ± 168^¥	176 ± 110^#	0.020274
18	Heterogeneous nuclear ribonucleoprotein H	hnRNP H1	P31943/HNRH1	198	22/55	59	394 ± 154^§	1424 ± 75^§¥#	238 ± 31^¥	141 ± 72^#	0.029005
23	PDZ and LIM domain protein 1	CLIM1	O00151/PDLI1	197	17/31	54	412 ± 115^$	313 ± 87	148 ± 29^$	325 ± 87	0.025707
30	26S proteasome non-ATPase regulatory subunit 8	PSMD8	P48556/PSMD8	104	7/9	16	71 ± 54^⁎	133 ± 79	79 ± 117	332 ± 134^⁎	0.039994
33	Ubiquitin carboxyl-terminal hydrolase isozyme L1	UCHL1	P09936/UCHL1	173	11/20	65	237 ± 75^§	95 ± 16^§	230 ± 92	116 ± 18	0.02802
35	Heat shock protein beta-1	HSP27	P04792/HSPB1	131	9/22	57	192 ± 198^⁎	361 ± 15	185 ± 20^&	557 ± 97^&⁎	0.020487
37	Heat shock protein beta-1	HSP27	P04792/HSPB1	82	5/8	28	89 ± 17^$	77 ± 23^¥	29 ± 8^$¥&	81 ± 10^&	0.006612
37	Heat shock protein beta-1	HSP27	P04792/HSPB1	LATQSNEITIPVTFESR			89 ± 17^$	77 ± 23^¥	29 ± 8^$¥&	81 ± 10^&	0.006612
38	40S ribosomal protein S12	RPS12	P25398/RS12	96	6/11	43	48 ± 16	70 ± 19^¥	27 ± 6^&¥	79 ± 5^&	0.010931
40	Eukaryotic translation initiation factor 1b	–	O60739/EIF1B	83	5/15	49	59 ± 42^⁎	68 ± 64^#	–	190 ± 9^⁎#	0.017554

Metabolism
11	Pyruvate kinase PKM	PKM2	P14618/KPYM	107	9/14	19	487 ± 120^§	1175 ± 319^§¥	227 ± 207^¥	–	0.000451
13	Inosine-5′-monophosphate dehydrogenase 2	IMD2	P12268/IMDH2	157	13/19	27	797 ± 97	328 ± 301^#	534 ± 306	1027 ± 19^#	0.025709
13	Inosine-5′-monophosphate dehydrogenase 2	IMD2	P12268/IMDH2	GKLPIVNEDDELVAIIAR			797 ± 97	328 ± 301^#	534 ± 306	1027 ± 19^#	0.025709
14	Succinyl-CoA:3-ketoacid coenzyme A transferase 1	SCOT	P55809/SCOT1	128	11/19	24	154 ± 112	151 ± 178	–	400 ± 117	0.047791
15	Aldehyde dehydrogenase X, mitochondrial	–	P30837/AL1B1	166	16/26	30	326 ± 61^⁎§$	143 ± 97^§	172 ± 37^$	63 ± 4^⁎	0.00606
22	Alcohol dehydrogenase [NADP(+)]	ALDX	P14550/AK1A1	195	16/30	52	382 ± 81	210 ± 72	–	383 ± 76	0.000186
29	S-methyl-5′-thioadenosine phosphorylase	MTAP	Q13126/MTAP	163	15/25	48	159 ± 41	106 ± 39^#	138 ± 49^&	264 ± 40^#&	0.013231
39	Coiled-coil-helix-coiled-coil-helix domain-containing protein 5	–	Q9BSY4/CHCH5	96	5/9	65	32 ± 23^⁎	27 ± 23^#	–	107 ± 53^⁎#	0.009274

Protein name in MetaCore network. Proteins excluded from the net according to the set parameters (–).

UniProt ID and entry name.

Each value represents the mean ± SD of individually computed %V in spot maps from control fibroblasts, and from fibroblasts obtained from OI patients carrying mutations in CRTAP, P3H1, or PPIB genes.

Pair-wise comparison was performed using the Tukey's post hoc test (p ≤ 0.05). Only proteins showing both statistical reliability and, at least, 2 fold change in expression are listed as significant differences: Control vs CRTAP (§); control vs P3H1 ($); control vs PPIB (*); CRTAP vs P3H1 (¥); CRTAP vs PPIB (#); P3H1 vs PPIB (&).