Water-soluble protein extracts (30 μg/lane) were run on 10% polyacrylamide gels and stained with Coomassie blue. Protein gels were then digitally scanned (Power LookII; Umax Data Systems, Inc., Industrial Park, Taiwan), and the density of each lane and each major band were measured with gel scanning software (1-D Gel Scan; MetaMorph; Universal Imaging Corp., Downingtown, PA). The percentage contribution of each major band to the total water-soluble protein for that sample was then determined by dividing the density of each band by the total density of each lane, after adjusting for background. Because individual proteins are compared to the total water-soluble protein level in each sample, providing an internal standard, minor differences in loading densities between samples are automatically corrected. In addition, when comparing cultured cells, calculating the percentage of water-soluble protein takes into account differences that may arise in cell volume between different keratocyte phenotypes that may influence the density of individual bands when comparing across cell phenotypes.
Major water-soluble proteins that comprised greater than 3.5% of the total water-soluble proteins were submitted for peptide sequence analysis to the Howard Hughes Medical Institute Biopolymer Facility at the University of Texas Southwestern Medical Center. Coomassie blue–stained polyacrylamide gels were provided to the facility, and the major bands were removed and processed on an ion-trap mass spectrometer (LCQ-DECA; Finnigan, San Jose, CA) equipped with an online capillary HPLC system (Waters, Milford, MA). Sequences were checked for homology to known protein sequences. The identity of selected proteins was then confirmed by Western blot analysis using rabbit anti-human ALDH1A1 (a gift from Ronald Lindahl, Department of Biochemistry, University of South Dakota, Vermillion, SD), rabbit anti-mouse TKT (a gift from Joram Piatigorsky, National Eye Institute, Bethesda, MD), rabbit anti-human ALDH3A1 (Ronald Lindahl), goat anti-human annexin II (Santa Cruz Biotechnology, Inc., Santa Cruz, CA), and anti-glyceraldehyde 3 phosphate dehydrogenase (G3PDH; Trevigen, Gaithersburg, MD).