Challenges in Bioinformatics Analysis for Metaproteomics

Abstract

Metaproteomics using mass spectrometry (MS) is a powerful method for classifying the very complex microorganisms in samples such as marine water, soil, feces, and saliva, and for profiling all the proteins expressed by all the microorganisms. Metagenomics can classify and profile the genes of the microorganisms in a sample, while metaproteomics can profile the proteins actually expressed to gain functional knowledge and understand what the microorganisms are doing. The analysis must be on a large scale, since the number of bacteria in the human intestine is larger than 1,000 species and 39 trillion, and the variety of species in each individual is very large. In this review, we discuss recent trends in metaproteomics of intestinal bacteria, including analysis software, protein sequence databases for intestinal bacteria, and issues related to large-scale analysis.