PXD021932

PXD021932 is an original dataset announced via ProteomeXchange.

Title	A Metaproteomic Workflow for Sample Preparation and Data Analysis Applied to Mouse Faeces: 4
Description	A Metaproteomic Workflow for Sample Preparation and Data Analysis Applied to Mouse Faeces: 1 MTD project_description Many diseases have been associated with gut microbiome abnormalities. The root cause of such diseases is not only due to bacterial dysbiosis, but also to change in bacterial functions, which are best studied by proteomic approaches. Although bacterial proteomics is well established, metaproteomics is hindered by challenges associated with the sample physical structure, contaminating proteins, the simultaneous analysis of hundreds of species and the subsequent data analysis. Here, we present a systematic assessment of sample preparation and data analysis methodologies applied to LC-MS/MS metaproteomics experiment. We could show that low speed centrifugation (LSC) has a significant impact on both peptide identifications and reproducibility. LSC led to increase in peptide and proteins identifications compare to no LSC. Notably, the dominant bacterial phyla, i.e. Firmicutes and Bacteroidetes, showed divergent representation between LSC and no-LSC. In terms of data processing, protein sequence databases derived from mouse faeces metagenome provided at least four times more MS/MS identification compared to databases of concatenated single organisms. We also demonstrated that two-steps database search strategy comes at the expense of a dramatic rise in number of false positives compared to single-step strategy. Overall, we found a positive correlation between matching metaproteome and metagenome abundance, which could be linked to core microbial functions, such as glycolysis-gluconeogenesis, citrate cycle and carbon metabolism. We observed significant overlap and correlation at the phylum, class, order and family taxonomic levels between taxonomy-derived from metagenome and metaproteome. Notably, nearly all functional categories (e.g., membrane transport, translation, transcription) were differentially abundant in the metaproteome (activity) compared to what would be expected from the metagenome (potential). In conclusion, these results highlight the need to perform metaproteomics when studying complex microbiome samples.
HostingRepository	PRIDE
AnnounceDate	2022-02-16
AnnouncementXML	Submission_2022-02-16_08:42:35.768.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nicolas Nalpas
SpeciesList	scientific name: mouse gut metagenome; NCBI TaxID: 410661;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2020-10-13 00:30:18	ID requested
⏵ 1	2022-02-16 08:42:36	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 Maček
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/PXD021932

PRIDE project URI

• PRIDE
  1. PXD021932
     1. Label: PRIDE project
     2. Name: A Metaproteomic Workflow for Sample Preparation and Data Analysis Applied to Mouse Faeces: 4