Cell walls of plants are complex structures impregnated with various proteins having wide array of functions. In this study, twenty-eight proteins isolated from tomato cell walls were subjected to MALDI-TOF MS followed by mass peak analysis using ORIGIN 6 software. The mass peaks subjected to MASCOT and ProFound databases for peptide mass fingerprinting led to the identification of 9 protein domains. These proteins were further classified according to their functions. Fruit extracts of A. indica could elicit induction, localization and functioning of peroxidase (POX) and polyphenol oxidase (PPO) and their isoenzymes in cell walls of Lycopersicum esculentum (tomato) against Pseudomonas syringae pv. tomato. The results revealed the possible involvement of cell wall-bound proteins in defence of plants against the invading pathogens. A number of novel isoenzymes of both POX and PPO were found to be located in the cell walls of the plants treated with neem extract. Neem extract can induce accumulation and binding of isoenzymes to cell walls. These isoenzymes could possibly protect host plants against the invading pathogens.