Proteome characterization of a human urothelial cell line resistant to the bladder carcinogen 4-aminobiphenyl

Table 1 Proteins identified by LC-MS/MS, showing different expression levels in the different cell lines. Detailed information on peptides/proteins identification is reported in Additional File 2.

Spot #	Protein identified	Symbol	Swiss-Prot	pI Theor./Exp.^b)	MW (kD) Theor./Exp.^b)	#pept. ^c)	Cov% ^d)	Score ^e)
46	Programmed cell death 6-interacting protein	PDCD6IP	Q8WUM4	6.13/6	96/95	15	17	93.9
146	Calreticulin	CALR	P27797	4.3/4.3	48/60	36	62	187.0
206	Aldehyde dehydrogenase 1A3 a	ALDH1A3a	P47895	6.9/6.4	56/56	20	25	108.6
207	Aldehyde dehydrogenase 1A3 b	ALDH1A3b	P47895	6.9/7	56/56	19	28	123
349	Elongation factor Tu	TUFM	P49411	7.3/7.5	49/46	12	30	64.2
431	3-Hydroxyisobutyl Coenzyme A hydrolase	HIBCH	Q53GA8	8.4/7.4	43/43	16
463	Glyceraldehyde-3-phosphate dehydrogenase	GAPDH	P04406	8.6/8	36/37	10	27	57.1
479	Annexin A2	ANXA2	P07355	7.6/8.7	38/37	11	33	81.5
680	Transgelin-2	TAGLN2	P37802	8.4/5.8	22/21	3	19	25.1
744	Fatty acid-binding protein	FABP4	P15090	6.8/6	14/14	39	73	145.9
801	Lamin-A/C	LMNA	P02545	6.6/6.2	74/75	35	41	197.6
841	94 kDa glucose-regulated protein	GRP94	P14625	4.7/4.7	92/95	15	18	105.2
906	NADH-ubiquinone oxidoreductase 30 kDa subunit	NDUFS3	O75489	6.9/5	30/28	10	46	84.3
912	Triosephosphate isomerase	TPI	P60174	6.5/6	26/27	12	42	77.1

^a) Arbitrary label assigned to the different isoforms.
^b) Theor.: theoretical, data-based annotations; Exp.: experimental, from 2-D gels.
^c) # pept.: number of valid peptide matches found for the given protein
^d) Cov%: the percent ratio of all amino acids from valid peptide matches to the total number of amino acids in the protein.
^e) Score: the protein score is a function calculated from the individual normalized z-scores of validated peptides. Peptide z-score refers to the distribution of calculated scores compared to that of random peptide sequences in order to find the mean and variance http://www.phenyx-ms.com. Database redundancy is handled and solved by the Phenyx software. If a protein shares all its validated peptides with another one, it is considered a subset and will not appear in the best-scoring protein list. It appears in the protein Details panel under Subset for the principal and better scoring parameters. Therefore the entries reported (Swiss_Prot AC) refer exclusively to the best-scoring protein found by the search engine.

ISSN: 1477-5956