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Metaproteomics focuses on protein levels
Compared to metagenomics and metatranscriptomics, metaproteomics has a lower depth of measurement and can only capture 10–20% of expressed proteins in human gut microbiomes
Metaproteomics is still in its infancy for the study of microbiomes. There is still a lack of universal guidelines and protocols for properly performing metaproteomic experiments and interpreting metaproteomic results. Therefore, careful considerations should be made for sample preparation, MS measurement, bioinformatic workflows, and data reporting
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