eMIS: Protein Modification Database and Flow Processing System of Chinese Human Liver Proteome Project

As an indispensable part of the Protein Modification Profiling effort in the Chinese Human Liver Proteome Project (CNHLPP), a protein modification data integrating and flow processing system named electronic Modification Information System (eMIS) has been established. The eMIS comprises a comprehensive protein modification database Moddb, a backend data processing pipeline, and a frontend data display and search web interface. Moddb currently contains nearly 13000 entries of protein modifications from phosphorylation, glycosylation, ubiquitinylation, etc. It is based on proteins other than residues, however, key information of modification sites on proteins are also recorded particularly in the database. The Moddb database also stores 3 different experimental protocols for protein modifications. The backend system processes the batch uploaded protein data, to build cross-references of the various data, and to store the raw data and processed results into Moddb. The web interface provides service of data upload, revising, searching, and also supports customization of experimental protocols. In summary eMIS is an integrative and comprehensive system supporting protein modification studies.