PXD078749

PXD078749 is an original dataset announced via ProteomeXchange.

Title	A streamlined high-throughput metaproteomic workflow for functional analysis of the rumen microbiome
Description	This project describes the development, optimization, and evaluation of a streamlined and scalable metaproteomic workflow for the functional characterization of the rumen microbiome. Rumen samples represent a highly complex biological matrix, and existing metaproteomic protocols are often labor-intensive and difficult to scale, limiting their application in large experimental studies. In this study, key steps of the metaproteomic pipeline were systematically assessed, including microbial cell extraction, cell lysis, protein digestion strategy, and LC–MS/MS acquisition parameters. The optimized workflow integrates a minimized cell extraction protocol starting from 0.5 g of rumen material, mechanical cell lysis using bead-based disruption, in-solution tryptic digestion, and short-gradient nanoLC–MS/MS analysis on an Orbitrap Fusion Lumos Tribrid mass spectrometer operated with FAIMS. The workflow was applied to a large set of samples originating from in vitro rumen fermentations, enabling assessment of both biological and technical variability. Results demonstrate robust taxonomic and functional profiling of the rumen microbiome, with biological variation dominating over technical variation and median coefficients of variation in the range of 21–24%. Overall, this dataset provides a resource supporting high-throughput functional investigations of rumen microbial ecosystems.
HostingRepository	PRIDE
AnnounceDate	2026-08-05
AnnouncementXML	Submission_2026-08-04_22:00:19.362.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ane Laura Fineid Pedersen
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: NEWT:9913;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2026-05-22 13:50:59	ID requested
⏵ 1	2026-08-04 22:00:19	announced

10.1016/J.JPROT.2026.105721;

submitter keyword: Rumen microbiome, Reproducibility,Metaproteomics, High-throughput workflow, Sample preparation, LC-MS/MS

Jana Seifert
contact affiliation	Holmir - Hohenheim Center for Livestock Microbiome Research, Functional microbiology of Livestock, University of Hohenheim, Stuttgart, germany
contact email	seifert.jana@uni-hohenheim.de
lab head
Ane Laura Fineid Pedersen
contact affiliation	Nesté Research
contact email	anelaurafineid.pedersen@rd.nestle.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/2026/08/PXD078749

PRIDE project URI

• PRIDE
  1. PXD078749
     1. Label: PRIDE project
     2. Name: A streamlined high-throughput metaproteomic workflow for functional analysis of the rumen microbiome