Metaproteomics has achieved several major advances with respect to sample preparation (Chapter 3.10), mass spectrometry (Chapter 3.2), labeling (Chapter 3.3), bioinformatics (Chapter 3.4), multi-omics data integration (Chapter 3.5), and model systems (Chapter 3.6), facilitating the identification of microbial effectors and their impact on microbiomes. However, several challenges also have to be considered while studying microbial effectors using metaproteomics (Figure ). limit of detection, LOQ: limit of quantification, DIA: data-independent acquisition, DDA: data-dependent acquisition, SIP: stable