Recovery of Extra-Radical Fungal Peptides Amenable for Shotgun Protein Profiling in Arbuscular Mycorrhizae

In arbuscular mycorrhizal symbiosis, the belowground mycelium that develops into the soil not only provides extensive pathways for nutrient and signal fluxes, the occupation of different niches and dispersal of propagules but also has strong influences upon biogeochemical cycling. By providing a valuable overview of protein expression, shotgun proteomics can help decipher key metabolic pathways involved in the functioning of fungal mycelia. In this protocol, we describe the combination of extra-radical mycelium growth systems with gel-based extraction of fungal peptides amenable to shotgun protein profiling, which allows gaining information about the extra-radical proteome together with its adaptive responses to environmental changes when associated with spectral counting.