PXD023217

PXD023217 is an original dataset announced via ProteomeXchange.

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

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.

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]

ProteomeXchange project tag: EPIC-XS

submitter keyword: microbial communities,metaproteomics, multi-omics

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

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

• PRIDE
  1. PXD023217
     1. Label: PRIDE project
     2. Name: Critical Assessment of Metaproteome Investigation (CAMPI): a Multi-Lab Comparison of Established Workflows