Table 1. Identified Peptide Isomers from Sheep Eye Lens Digest^a,

peptide sequence	crystallin	number of peaks in LC separation	relative abundance (%)f	number of peptide isomers confirmed by MS/MSb
Ac-1MDIAIQHPWF K11c	αA	4	3.7%, 1.2%, 93.9%, 1.2%	4
22LFDQFFGEGL FEYDLLPFLSSTISPYYR49	αA	3	7.8%, 32.4%, 59.8%	3
55TVLDSGISEV R65	αA	3	47.4%, 50.8%, 1.8%	4g,i
79HFSPEDLTVK88	αA	2	10.4%, 89.6%	2
89VQEDFVEIHG K99	αA	1		2
104QDDHGYISR112d,e	αA	5	4.7%, 21.1%, 15.1%, 3.1%, 56.0%	4
132SLSADGMLTF SGPK145	αA	2	13.7%, 86.3%	2
146VPSGVDAGHS ER157	αA	3	8.7%, 53.3%, 38.0%	3
164EEKPSSAPSS173e	αA	3	11.8%, 82.3%, 5.9%	3
Ac-1MDIAIHHPWI R11	αB	2	9.1%, 91.9%	2
23LFDQFFGEHL LESDLFPAST SLSPF47	αB	2	9.3%, 90.7%	2
57APSWIDTGLS E MR69	αB	6	1.6%, 34.0%, 1.0%, 1.8%, 59.7%, 1.9%	4
108QDEHGFISR116d,e	αB	2	4.2%, 95.8%	2
124IPADVDPLTI TSSLSSDGVL TVNGPR149	αB	1		2
Ac-2AEQHSAPEQA AAGK15c	βB3	1		2i
39C**ELTAEC**PNL TESLLEK55h	βB3	2	14.2%, 85.8%	2
89WDAWSNSHHSDSLL102	βB3	1		2
103SLRPLHIDGP DHK115	βB3	1		2
129MEIVDDDVPS LWAHGFQDR147	βB3	1		2
180HWNEWDANQP QLQSVR195	βB3	1		2

^aSingle letter codes are used for amino acids. Underlined residues correspond to most likely sites of epimerization. Bold residues are likely sites of isomerization. The UniprotKB Accession Numbers for the identified proteins are αA crystallin, Q5ENZ0, αB crystallin, W5Q0R4, and βB3 crystallin, Q52NW3.

^bFor peptides observed in multiple HPLC peaks, MS/MS spectra are compared carefully to confirm the number of peptide isomers.

^cAc- represents N-terminal acetylation.

^dN-terminal glutamine cyclization.⁴³

^eThese peptides were identified by searching the data against a smaller database as detailed in the Experimental Methods section above.

^fCalculated from peak area in the extracted ion chromatogram.

^gDetermined from the combination of RDD and CID results.

^hThe double star represents iodoacetamide modified cysteine (+57 Da).

ⁱIsomers were confirmed by comparison with synthetic peptides.