PXD027306

PXD027306 is an original dataset announced via ProteomeXchange.

Title	A Metaproteomic Workflow for Sample Preparation and Data Analysis Applied to Mouse Faeces: 5
Description	The intestinal microbiota plays a key role in shaping host homeostasis by regulating metabolism, immune responses and behaviour. Its dysregulation has been associated with metabolic, immune and neuropsychiatric disorders and is accompanied by changes in bacterial metabolic regulation. Although proteomic is well suited for analysis of individual microbes, metaproteomic of faecal samples is challenging due to the physical structure of the sample, presence of contaminating host proteins and coexistence of hundreds of species. Furthermore, there is a lack of consensus regarding preparation of faecal samples, as well as downstream bioinformatic analyses following metaproteomic data acquisition. Here we assess sample preparation and data analysis strategies applied to mouse faeces in a typical LC-MS/MS metaproteomic experiment. We show that low speed centrifugation (LSC) of faecal samples leads to high protein identification rates but possibly enriched for a subset of taxa. During database search, two-step search strategies led to dramatic and underestimated accumulation of false positive protein identifications. Regarding taxonomic annotation, the MS-identified peptides of unknown origin were annotated with highest sensitivity and specificity using the Unipept software. Comparison of matching metaproteome and metagenome data revealed a positive correlation between protein and gene abundances. Notably, nearly all functional categories of detected protein groups were differentially abundant in the metaproteome compared to what would be expected from the metagenome, highlighting the need to perform metaproteomic when studying complex microbiome samples.
HostingRepository	PRIDE
AnnounceDate	2022-02-17
AnnouncementXML	Submission_2022-02-17_05:27:42.089.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nicolas Nalpas
SpeciesList	scientific name: Archaea; NCBI TaxID: 2157; scientific name: Viruses; NCBI TaxID: 10239; scientific name: Eukaryota; NCBI TaxID: 2759; scientific name: Bacteria; NCBI TaxID: 2;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-07-14 07:37:37	ID requested
⏵ 1	2022-02-17 05:27:43	announced

Nalpas N, Hoyles L, Anselm V, Ganief T, Martinez-Gili L, Grau C, Droste-Borel I, Davidovic L, Altafaj X, Dumas ME, Macek B, An integrated workflow for enhanced taxonomic and functional coverage of the mouse fecal metaproteome. Gut Microbes, 13(1):1994836(2021) [pubmed]

submitter keyword: Metaproteomics, Mus musculus, Metagenome, Taxonomy

Prof. Dr. Boris Macek
contact affiliation	Quantitative Proteomics Proteome Center Tübingen Universität Tübingen Auf der Morgenstelle 15 72076 Tübingen
contact email	boris.macek@uni-tuebingen.de
lab head
Nicolas Nalpas
contact affiliation	Tuebingen University
contact email	nalpas.nicolas@gmail.com
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/PXD027306

PRIDE project URI

• PRIDE
  1. PXD027306
     1. Label: PRIDE project
     2. Name: A Metaproteomic Workflow for Sample Preparation and Data Analysis Applied to Mouse Faeces: 5