PurposeIn this study, by using a two-dimensional (2D) electrophoresis-based experimental approach, we aimed at understanding the nature of alkali injuries and the underlying mechanisms. A secondary aim was to compare the effects of cross-linking (CXL) and amnion membrane transplantation (AMT) on corneal protein compositions at the end of the early repair phase after injured with alkali.MethodThe right corneas of 24 rabbits were injured with a 1N solution of NaOH. Groups were formed based on the adjuvant therapies as (1) healthy group, (2) control group, (3) CXL group, (4) AMT group. In addition to the therapies, a conventional medical treatment was applied to all groups. Left eyes were used as within-subject healthy corneas (1). The corneas were excised at day 21, and a comparative proteomic analysis was performed using 2D gel electrophoresis coupled with MALDI-TOF/TOF.Result2D gel electrophoresis revealed the presence seven protein spots whose abundance changed among the groups. Those proteins were SH3 domain-binding protein, plant homeodomain finger protein 23, S100 calcium binding protein A-11(S100 A11), keratin type 2 cytoskeletal 1 and 2, transketolase and glyceraldehyde 3-phosphate dehydrogenase. Ingenuity pathway analysis predicted that the observed changes may be linked to a central metabolic pathway, transforming growth factor beta 1. Canonical pathway analysis focused our attention to two different pathways, namely nicotinamide adenine dinucleotide repair pathway and non-oxidative branch of pentose phosphate pathway.ConclusionOur results shed some light onto the molecular mechanisms affected by alkali injury and adjuvant treatments. Further research is needed to propose medically significant target molecules that may be used for novel drug developments for alkali injury.