Microbial communities are complex biological assemblies that are widely distributed on/in human bodies and various environments such as soil, marine and freshwater, sediments, etc. Proteomics, which has many advantages over genomics, is currently used to obtain protein catalogues, yield qualitative and quantitative information about proteins, and compare protein contents in different ecosystems. Therefore, proteomics research is now being greatly engaged in the microbial field. We summarized the advantages, main application fields, and workflow of proteomics in microbial research in the attachment. And we reviewed the currently used protein quantification methods that can greatly facilitate your microbial proteomics research.