Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows.
Tim Van Den BosscheBenoit Josef KunathKay SchallertStephanie S SchäpePaul E AbrahamJean ArmengaudMagnus Øverlie ArntzenAriane BassignaniDirk BenndorfStephan FuchsRichard J GiannoneTimothy J GriffinLive Heldal HagenRashi HalderCéline HenryRobert L HettichRobert HeyerPratik D JagtapNico JehmlichMarlene JensenCatherine JusteManuel KleinerOlivier LangellaTheresa LehmannEmma LeithPatrick MayBart MesuereGuylaine MiotelloSamantha L PetersOlivier PiblePedro T QueirosUdo ReichlBernhard Y RenardHenning SchiebenhoeferAlexander SczyrbaAlessandro TancaKathrin TrappeJean-Pierre TrezziSergio UzzauPieter VerschaffeltMartin Von BergenPaul WilmesMaximilian WolfLennart MartensThilo MuthPublished in: Nature communications (2021)
Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out a community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluate the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observe that variability at the peptide level is predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappear at the protein group level. While differences are observed for predicted community composition, similar functional profiles are obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.
Keyphrases
- endothelial cells
- mass spectrometry
- healthcare
- mental health
- induced pluripotent stem cells
- pluripotent stem cells
- liquid chromatography
- machine learning
- binding protein
- current status
- molecularly imprinted
- big data
- high performance liquid chromatography
- clinical evaluation
- amino acid
- gas chromatography
- deep learning
- decision making
- simultaneous determination
- solid phase extraction