Metaproteomics

The present book aims to be the reference for the proteomic methods of microbial com- munities (metaproteomics). It has been thought for M.Sc. and Ph.D. students in biology, chemistry, ecology, medicine, environmental sciences, and everyone who would like to apply this approach for his scientific investigations. In last years, metagenomics gave many elucidations about the composition and taxon- omy of microbial consortia difficult to understand with classical approaches, while meta- transcriptomics represented a powerful approach to deepen their potential functional aspects. Nevertheless, the effective functionality can be given by the protein patterns in a specific moment or condition through metaproteomics. In this book, the metaproteomic techniques are presented first focusing on the methods of sampling and protein extractions from different environments and/or ecological niches crowded by heterogeneous microbial communities. Extractions and possible purifications of proteins are very critical methodological steps for a good metaproteomic approach, and they can differ depending on the kind and origin of the sample. The chapters of the second part of the book concern the complete metaproteomic workflows of microbial communities in different situations or conditions, including the corresponding and more appropriate mass spectrometry and bioinformatic analyses. Some- times, a representative case has been used as an example for the related protocol description and explanation; however, the described procedure can be applied to microbial consortia in the similar environment or condition. In the last chapter, an overview of bioinformatic pipelines specific for metaproteomics are described aiming to an optimal elaboration and interpretation of results.