Metaproteomics is a powerful method to acquire in-depth data on microbiomes, with the human gut microbiome being of particular interest to researchers. LC-MS/MS-based metaproteomics is used to characterize taxonomic and functional microbiome composition in the field of health, environmental sciences, and biotechnology. The abundance of proteins generally correlates well with actual activity and can detect proteins from the environment, such as host protein in the human gut or substrate proteins in biogas plants. The long-term goal of the metaproteomics research community is to contribute to the complete exploration of the human gut microbiome and to offer an attractive option for routine diagnostics. Standardization and data integration are key milestones toward this goal. Routine diagnostics is only feasible if a large enough body of data is available. In principle, this data already exists, but further efforts of data integration have to be undertaken. The Use Case MetaProt aims at standardization and data integration in human gut metaproteomics by achieving two objectives: 1. the creation of a curated protein sequence database of the human gut microbiome, and 2. the creation of a metadata annotation and file conversion tool that produces a uniform output from diverse sources of experimental data.
Graphical abstract “Use Case MetaProt” by Dirk Benndorf, Robert Heyer and Kay Schallert with visual adaptation by Maja Magel is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).
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Below, you will find the output provided by the Use Case. If you are interested in the development stages of the project, these are indicated by the following tenses and suffixes.
The output for the research community is already established (-ed for past tense), is currently being (-ing for present progressive) in progress, or will be soon set-up (present tense) for future endeavors.