Two-dimensional (2D) gel electrophoresis affords us a qualitative view of the proteome of an organism, which offers a rich understanding of the molecular weight and isoelectric points of proteins expressed under given environmental and nutritional conditions. But, clustering of proteins of similar molecular weight or isoelectric point or both makes separation of proteins difficult. To this end, a theoretical 2D protein gel calculated based on experimental proteome of an organism would provide important clues to the ability of 2D gel electrophoresis to separate two target proteins. More importantly, a theoretical 2D gel is a visualisation of the distribution of isoelectric points and molecular weights of all proteins in the species, which is important to gaining an approximate but high-level understanding of the physiological properties of the organism. This work presents the theoretical 2D protein gel of Helicobacter pylori.