Benchmarking the current state of metaproteomics : a community driven evaluation of experimental and computational techniques
- Metaproteomics has substantially grown over the past years and supplements other omics approaches by bringing valuable functional information, enabling genotype- phenotype linkages and connections to metabolic outputs. Currently, a wide variety of metaproteomic workflows is available, yet their impact on the results remains to be thoroughly assessed.
Here, we carried out the first community-driven, multi-lab comparison in metaproteomics: the critical assessment of metaproteome investigation (CAMPI) study. Based on well-established workflows, we evaluated the influence of sample preparation, mass spectrometry acquisition, 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 workflows were the most important source of differences between analyses. Overall, these peptide-level differences largely disappeared at the proteinMetaproteomics has substantially grown over the past years and supplements other omics approaches by bringing valuable functional information, enabling genotype- phenotype linkages and connections to metabolic outputs. Currently, a wide variety of metaproteomic workflows is available, yet their impact on the results remains to be thoroughly assessed.
Here, we carried out the first community-driven, multi-lab comparison in metaproteomics: the critical assessment of metaproteome investigation (CAMPI) study. Based on well-established workflows, we evaluated the influence of sample preparation, mass spectrometry acquisition, 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 workflows were the most important source of differences between analyses. Overall, these peptide-level differences largely disappeared at the protein group level. Differences were observed between peptide- and protein-centric approaches for the predicted community composition but similar functional profiles were found across workflows.
The CAMPI findings demonstrate the robustness of current metaproteomics research and provide a perspective for future benchmarking studies.…
Autor*innen: | Thilo MuthORCiD |
---|---|
Dokumenttyp: | Vortrag |
Veröffentlichungsform: | Präsentation |
Sprache: | Englisch |
Jahr der Erstveröffentlichung: | 2021 |
Organisationseinheit der BAM: | VP Vizepräsident |
VP Vizepräsident / VP.1 eScience | |
DDC-Klassifikation: | Naturwissenschaften und Mathematik / Chemie / Analytische Chemie |
Freie Schlagwörter: | Benchmarking; Bioanalytics; International lab study; Mass spectrometry; Metaproteomics |
Themenfelder/Aktivitätsfelder der BAM: | Chemie und Prozesstechnik |
Veranstaltung: | ISMB/ECCB 2021 |
Veranstaltungsort: | Online meeting |
Beginndatum der Veranstaltung: | 28.07.2021 |
Verfügbarkeit des Dokuments: | Datei im Netzwerk der BAM verfügbar ("Closed Access") |
Datum der Freischaltung: | 22.12.2022 |
Referierte Publikation: | Nein |
Eingeladener Vortrag: | Nein |