PXD054260

PXD054260 is an original dataset announced via ProteomeXchange.

Title	Improving protein extraction for metaproteomic analysis of marine sediment with high clay content
Description	Marine sediments harbor highly diverse microbial communities that contribute to global biodiversity and play essential roles in the ecosystem functioning. However, the metaproteome of marine sediments remains poorly understood. Extracting proteins from environmental samples can be challenging, especially in marine sediments due to their complex matrix. Few studies have been conducted on improving protein extraction methods from marine sediments. To establish an effective protein extraction workflow for clay-rich sediments, we compared, combined and improved several protein extraction methods. The presented workflow includes blocking of protein binding sites on sediment particles with high concentrations of amino acids, effective cell lysis via ultra-sonication, and the electro-elution and simultaneous fractionation of proteins. Using this workflow, we were able to recover 100% of the previously added Escherichia coli proteins from the sediment.
HostingRepository	PRIDE
AnnounceDate	2025-05-12
AnnouncementXML	Submission_2025-05-12_05:18:20.599.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Anke Trautwein-Schult
SpeciesList	scientific name: unclassified Bacteria (miscellaneous); NCBI TaxID: 49928;
ModificationList	iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-25 22:57:30	ID requested
⏵ 1	2025-05-12 05:18:21	announced

10.1093/ISMECO/YCAF074;

submitter keyword: Metaproteomics

marine sediment

protein extraction

Dörte Becher
contact affiliation	Institute of Microbiology, Department of Microbial Proteomics, University of Greifswald, Germany
contact email	dbecher@uni-greifswald.de
lab head
Anke Trautwein-Schult
contact affiliation	University of Greifswald
contact email	anke.trautwein-schult@uni-greifswald.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/2025/05/PXD054260

PRIDE project URI

• PRIDE
  1. PXD054260
     1. Label: PRIDE project
     2. Name: Improving protein extraction for metaproteomic analysis of marine sediment with high clay content