Soil and litter metaproteomics, assigning soil and litter proteins to specific phylogenetic and functional groups, has a great potential to shed light on the impact of microbial diversity on soil ecosystem functioning. However, metaproteomic analysis of soil and litter is often hampered by the enormous heterogeneity of the soil matrix and high concentrations of humic acids. To circumvent these challenges, sophisticated protocols for sample preparation have to be applied. This chapter provides the reader with detailed information on well-established protocols for protein extraction from soil and litter samples together with protocols for further sample preparation for subsequent MS analyses.
Keywords: Homogenization; In-gel digestion; Interfering substances; Matrix effects; Protein separation; Reducing sample complexity; SDS-PAGE; Soil sampling.