In contrast, soil or wastewater sludge samples contain high amounts of organic and phenolic compounds, polymeric substances, and inorganic compounds (including minerals), necessitating specialized purification and extraction protocols. Proteins can be adsorbed onto solid particles, such as clay minerals, which are often only partially reversible. The extracted proteome can be further fractionated to enable deeper proteome coverage and identification of low abundant microbial effectors, either before proteolytic digestion (e.g., via gel electrophoresis) or afterward (e.g., ion exchange chromatography) . However, direct analysis without fractionation and using 1D separation often provides sufficient coverage of the central metabolic pathways of the most abundant taxa . This approach also saves significant time when analyzing large sample cohorts, such as in clinical studies. A particular challenge is posed by phages, hydrolytic enzymes or small peptides secreted into the extracellular environment. These require efficient extraction, concentration, and purification from often complex matrix components combined with enrichment of target molecules (e.g., antimicrobial glycopeptides) to achieve sensitive detection.