PXD057908-1

PXD057908 is an original dataset announced via ProteomeXchange.

Title	FISH-FACS Proteomics: Enhanced label-free quantitative proteome analysis from ultra-low cell numbers of environmental microorganisms
Description	Metaproteomics is an essential approach to analyse the in situ metabolic activity of microbes across various environments. In such highly diverse environmental samples, the functionality of specific microorganisms of importance often remains underexplored due to the protein inference problem arising from sequence homologies between organisms. One approach to overcome this challenge is the enrichment of non-culturable target organisms. However, this often result in samples with low protein content. In this study, we have developed a workflow that combines fluorescence in situ hybridisation (FISH) and fluorescence-activated cell sorting (FACS) with mass spectrometry-based proteomics to analyse proteins from non-culturable bacteria directly from environmental samples. We show that 1x105 cells are sufficient for reliable qualitative protein identifications, while 5x105 to 1x106 cells allow for reproducible protein quantification after FISH and FACS. Furthermore, the use of a taxon-specific database improves data analysis by significantly reducing the size of protein groups compared to metaproteomics data.
HostingRepository	PRIDE
AnnounceDate	2025-09-29
AnnouncementXML	Submission_2025-09-29_04:03:23.251.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sandra Maass
SpeciesList	scientific name: Polaribacter sp.; NCBI TaxID: 1920175; scientific name: Aurantivirga; NCBI TaxID: 1737068;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-14 16:31:29	ID requested
⏵ 1	2025-09-29 04:03:24	announced

10.1093/ismeco/ycaf145;

Kale V, Ho GYG, Maa, ß S, Trautwein-Schult A, Bartosik D, Schweder T, Fuchs BM, Becher D, FISH-FACS proteomics: enhanced label-free quantitative proteome analysis from low cell numbers of uncultured environmental microorganisms. ISME Commun, 5(1):ycaf145(2025) [pubmed]

submitter keyword: microbial ecology, Polaribacter spp., Aurantivirga sp.,marine microorganisms

Dörte Becher
contact affiliation	Institute of Microbiology, University of Greifswald, 17489 Greifswald, Germany
contact email	dbecher@uni-greifswald.de
lab head
Sandra Maass
contact affiliation	University of Greifswald, Department for Microbial Proteomics
contact email	sandra.maass@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/2025/09/PXD057908

PRIDE project URI

• PRIDE
  1. PXD057908
     1. Label: PRIDE project
     2. Name: FISH-FACS Proteomics: Enhanced label-free quantitative proteome analysis from ultra-low cell numbers of environmental microorganisms