PXD023217
PXD023217 is an original dataset announced via ProteomeXchange.
Dataset Summary
Title | Critical Assessment of Metaproteome Investigation (CAMPI): a Multi-Lab Comparison of Established Workflows |
Description | Metaproteomics, the study of the collective proteome within a microbial ecosystem, has substantially grown over the past few years. This growth comes from the increased awareness that it can powerfully supplement metagenomics and metatranscriptomics analyses. Although metaproteomics is more challenging than single-species proteomics, its added value has already been demonstrated in various biosystems, such as gut microbiomes or biogas plants. Because of the many challenges, a variety of metaproteomics workflows have been developed, yet it remains unclear what the impact of the choice of workflow is on the obtained results. Therefore, we set out to compare several well-established workflows in the first community-driven, multi-lab comparison in metaproteomics: the critical assessment of metaproteome investigation (CAMPI) study. In this benchmarking study, we evaluated the influence of different workflows on sample preparation, mass spectrometry acquisition, and bioinformatic analysis on two samples: a simplified, lab-assembled human intestinal sample and a complex human fecal sample. We find that the same overall biological meaning can be inferred from the metaproteome data, regardless of the chosen workflow. Indeed, taxonomic and functional annotations were very similar across all sample-specific data sets. Moreover, this outcome was consistent regardless of whether protein groups or peptides, or differences at the spectrum or peptide level were used to infer these annotations. Where differences were observed, those originated primarily from different wet-lab methods rather than from different bioinformatic pipelines. The CAMPI study thus provides a solid foundation for benchmarking metaproteomics workflows, and will therefore be a key reference for future method improvement. |
HostingRepository | PRIDE |
AnnounceDate | 2023-05-14 |
AnnouncementXML | Submission_2023-05-14_14:17:25.595.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | KaySchallert |
SpeciesList | scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Q Exactive HF; Orbitrap Fusion Lumos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
---|---|---|---|
0 | 2020-12-18 01:48:37 | ID requested | |
1 | 2022-02-16 13:39:35 | announced | |
⏵ 2 | 2023-05-14 14:17:26 | announced | 2023-05-14: Updated project metadata. |
Publication List
Van Den Bossche T, Kunath BJ, Schallert K, Sch, ä, pe SS, Abraham PE, Armengaud J, Arntzen M Ø, Bassignani A, Benndorf D, Fuchs S, Giannone RJ, Griffin TJ, Hagen LH, Halder R, Henry C, Hettich RL, Heyer R, Jagtap P, Jehmlich N, Jensen M, Juste C, Kleiner M, Langella O, Lehmann T, Leith E, May P, Mesuere B, Miotello G, Peters SL, Pible O, Queiros PT, Reichl U, Renard BY, Schiebenhoefer H, Sczyrba A, Tanca A, Trappe K, Trezzi JP, Uzzau S, Verschaffelt P, von Bergen M, Wilmes P, Wolf M, Martens L, Muth T, Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nat Commun, 12(1):7305(2021) [pubmed] |
Keyword List
ProteomeXchange project tag: EPIC-XS |
submitter keyword: microbial communities,metaproteomics, multi-omics |
Contact List
ThiloMuth | |
---|---|
contact affiliation | Section eScience (S.3), Federal Institute for Materials Research and Testing, Berlin, Germany Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany |
contact email | thilo.muth@bam.de |
lab head | |
KaySchallert | |
contact affiliation | Otto-von-Guericke University Magdeburg |
contact email | kay.schallert@ovgu.de |
dataset submitter |
Full Dataset Link List
Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/02/PXD023217 |
PRIDE project URI |
Repository Record List
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