Critical Assessment of Metaproteome Investigation (CAMPI): a Multi-Lab Comparison of Established Workflows. CAMPI

Metaproteomics has substantially matured over the past years as a powerful tool to assess functional interactions in microbial communities. A wide variety of metaproteomic workflows is available, yet their impact on the results remains to be established.Here, we carried out the first community-driven, multi-lab comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluated the influence of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, lab-assembled human intestinal model and a human fecal sample.Although bioinformatic pipelines contributed to variability in peptide identification, wet-lab stages were the most important source of differences between analyses. Moreover, protein groups were less sensitive to those differences than peptides. Comparing taxonomic and functional profiles revealed differences between peptide- and protein-centric approaches at the taxonomic level but very similar functional profiles.These CAMPI findings present the current opportunities and challenges in metaproteomics research and provide a perspective for future benchmarking studies.