The colon is inhabited by circa ten bacteria for each cell of our organism (microbiota) and it is estimated that, altogether, they posses between 100 to 150 times more genes (microbiome) that the human genome. Between these two sets of genomes, acting as a biological interface, there is a mucus bilayer biochemically structured by the Mucin 2 glycoprotein. Several analytical proteomics strategies are presented in this study, which contribute to the proteomic map of human intestinal mucus, enlarging knowledge of this important sample. Utilizing mucus obtained from sampling via a transanal irrigation procedure, 15 different protocols for running the samples through 2-D PAGE in the pH ranges 3-10 or 4-7 were evaluated. The protocol that showed no streaking in 2-D PAGE and yielded more protein spots (116 and 220 spots were found in the 3 to 10 and 4 to 7 pH ranges, respectively) was considered the best and was the one that was finally used (protocol C). For improving protein identification, SDS-PAGE, 2-D PAGE and shotgun proteomics are carried out through nLC-MS/MS, and a Venn diagram built-up from identified proteins as well as cellular, bacterial and other proteins of clinical interest. Mucin 2, which is the main component of the mucus, is accurately identified, despite its insolubility and high molecular weight, indicating the complementarity and the success of the optimization conditions of all strategies employed. Finally, the interaction between 23 identified proteins is carried out, indicating two major classes of proteins: energy metabolism and energy consumption.