Helicobacter pylori is an important human gastric pathogen that has been studied by the relatively new technique of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). This work attempts to annotate the mass peaks of two strains of H. pylori (J99 and ATCC 26695) that has been reported in the literature in 2010 out of pure curiosity. Reference proteome used in this work was H. pylori proteome deposited in UniProt, and the annotation process taken was aided by an in-house MATLAB mass peak annotation software. Briefly, the mass peaks reported were compared to the molecular weight of each protein in the H. pylori proteome to help find a match of lowest error in molecular weight. Results revealed that most of the annotated mass peaks were from ribosomal proteins, especially those in the large ribosome subunit. Other annotated proteins were uncharacterised proteins, which suggest that important facet of this important H. pylori pathogen remains unknown to the biology and biomedical community. Overall, annotation of the mass peaks of two strains of H. pylori should provide a useful resource for other works trying to understand the origins of the mass peaks and their physiological roles in the organism and in human pathogenesis.