TABLE 1.

Protein Regions Observed and Level of Coverage for Protein Fragments

					Residue Endpoints
Protein Name	Swiss-Prot Accession Number	Spot	DB MW (kDa)	Gel MW (kDa)	N	C	Protein Region	Protein N-Terminala	Coverageb (%)	Weighted Coveragec (%)
Cathepsin D	P07339	8	45	27	177	411	NA	C-term.	30	51
		9	45	27	177	411	NA	C-term.	17	29
Chymotrypsinogen B	P17538	16	28	28	80	125	ND	full	14
		17	28	17	19	125	-signal	N-term.	20	33
		18	28	17	19	125	-signal	N-term.	20	33
		19	28	15	80	125	NA	central	14	26
		20	28	15	80	125	NA	central	14	26
GRp78 d	P11021	21	72	72	50	633	ND	full	37
		22	72	48	50	386	ND	N-term.	28	41
		23	72	48	50	386	ND	N-term.	28	41
		24	72	25	447	633	NA	C-term	12	35
α-Amylase 2A	P04746	27	58	16	16	155	-signal	N-term.	12	43
		28	58	10	177	210	NA	central	6	36
Pancreatic lipase related protein 2	P54317	30	52	52	44	334	-signal	full	15
		31	52	31	44	251	-signal	N-term.	9	16
Prolyl 4-hydroxylase β	P07237	34	57	57	18	461	-signal	full	42
		35	57	37	18	338	-signal	N-term.	20	31
		36	57	25	18	230	-signal	N-term.	14	32
Heat shock cognate protein 71 kDad	P11142	40	71	37	26	342	ND	N-term.	17	33
Cytokeratin 8	P05787	43	54	17	264	391	NA	central	19	60
Actin, β and γe	P60709, P63261	56	42	40	19	372	ND	full	31
		59	42	26	197	372	NA	C-term.	10	17
14-3-3 ζ	P63104	66	28	17	28	41	NA	N-term.	6	9

^a Detection of the protein N-terminal peptide for each gel spot. –signal indicates that the N-terminal peptide was detected with the signal sequence removed; NA:not applicable for protein fragments that do not cover the N-terminal of the protein or protein lacking a signal sequence; ND: not detected in the MS.

^b (# of amino acid residues identified in MS/# of amino acids in database protein sequence) × 100.

^c coverage for fragments is weighted by the MW of the gel spot, calculated as (% coverage) × (database MW of full-length protein / observed gel MW of protein fragment).

^d Two proteins were previously reported under different names¹⁴: GRP78 was listed under the gene name HSPA5 and heat shock cognate protein 71 kDa under heat shock cognate protein 54 kDa. The names have been changed to be consistent with the Swiss-Prot names listed for these accession numbers.

^e β and γ isoforms not distinguishable with our MS data.