Rag2-/-Il10-/- mice were subjected to infection by Helicobacter hepaticus and allowed to develop long-term infections. Proximal colon tissue was then harvested from the mice for analysis. RNA was isolated from the samples and submitted for transcriptomic analysis; this data was then used to create a custom RNA-based FASTA database. Protein isolated from the proximal colon samples were digested and analyzed via bottom-up mass spectrometry. The custom FASTA database was then used for proteogenomic analysis of the raw mass spectrometry data in the Galaxy for proteomics (Galaxy-P) platform.