There are many papers containing assay methods. The first ones I saw used extracts from cells scraped from animal stomachs (example: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3326759/). Are you looking for a method like this, or do you intend to work with a purified, reconstituted protein or an overexpressing cell line? Do you want to measure ATP hydrolysis or proton pumping? How many compounds do you need to test?

Here is a paper that describes a high-throughput screen for gastric proton pump inhibitors: http://jbx.sagepub.com/content/17/2/177.full.pdf+html