Candidate autoantigens identified by mass spectrometry in early rheumatoid arthritis are chaperones and citrullinated glycolytic enzymes

Table 2 Identities of immunoreactive spots from MALDI-TOF spectra using the Aldente and FindMod tools

Protein	Swiss-Prot number	Theoretical MW (Da)/pI	Hits^a		Coverage (%)^b		Aldente score^c	Aldente Z score^d
			Aldente	FindMod	Aldente	FindMod
Heterogeneous nuclear ribonucleoprotein A2/B1	[Swiss-Prot:P22626]	37,430/9.0	17	21	51	51	49.54	655.1
Aldolase	[Swiss-Prot:P04075]	39,288/8.4	22	60	69	86	44.36	814.8
Top of form 1 phosphoglycerate kinase 1	[Swiss-Prot:P00558]	44,728/8.3	15	25	40	54	21.20	416.8
α-Enolase	[Swiss-Prot:P06733]	47,169/7.0	12	33	39	59	16.19	208.2
Calreticulin	[Swiss-Prot:P27797]	48,142/4.3	16	51	36	51	20.14	99.5
Heat shock protein 60	[Swiss-Prot:P10809]	61,055/5.7	26	41	52	64	107.28	1389
Stress-induced phosphoprotein 1	[Swiss-Prot:P31948]	62,638/6.4	19	31	38	49	36.04	898.2
FUSE-BP1	[Swiss-Prot:Q96AE4]	67,474/7.2	15	23	30	35	41.78	402.7
FUSE-BP2	[Swiss-Prot:Q92945]	72,708/8.2	12	23	22	25	13.64	171.4
BiP	[Swiss-Prot:P11021]	72,334/5.1	25	34	44	47	94.41	1616.3

FUSE-BP, far-upstream element-binding protein; MALDI-TOF, matrix-assisted laser desorption/ionization–time of flight; MW, molecular weight; pI, isoelectric point. ^aA hit is an experimental peak matching a theoretical peptide. ^bThe coverage is the number of amino acids present in at least one peptide/the number of amino acids of the protein. ^cThe Aldente tool gives a score to each identified protein. The parameters selected in these scores are the number and the intensity of hits, the number of missed cleavages, the C-terminal amino acid, the chemical modifications and, at the protein level, the coverage of the identified peptides on the sequence. The score of the proteins identified in this study are largely greater than the score of the best random protein. ^dThe Z score is the number of standard deviations for a given score from the mean random score.

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