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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.
KEY COMPARISON
At the October 2005 CCQM Organic Analysis Working Group Meeting (IRMM, Belgium), the decision was made to proceed with a Key Comparison study (CCQM-K47) addressing the calibration function for the determination of volatile organic compounds (VOCs) used for water quality monitoring. This was coordinated by CENAM and NIST. Benzene, o-xylene, m-xylene and p-xylene were chosen as representative VOCs. The solvent of choice was methanol.
Key Comparison CCQM-K47 demonstrated the capabilities of participating NMIs to identify and measure the four target VOCs in a calibration solution using GC-based methods. The measurement challenges in CCQM-K47, such as avoiding volatility loss, achieving adequate chromatographic resolution and isolating potential interferences, are typical of those required for value-assigning volatile reference materials. Participants achieving comparable measurements for all four VOCs in this Key Comparison should be capable of providing reference materials and measurements for VOCs in solutions when present at concentration levels greater than 10 µg/g.