PXD071909-1

PXD071909 is an original dataset announced via ProteomeXchange.

Title	Characterization of extracellular vesicles from cell suspension 2 cultures of Coffea arabica L.
Description	A protocol was developed for the isolation and characterization of extracellular vesicles (EVs) from Coffea arabica cell suspension cultures (CSC). The isolation method involved differential ultracentrifugation of the CSC filtrate, yielding two fractions: 100,000 g for 36 minutes (100k g) and 125,000 g for 6 hours (125k g). Both fractions were characterized by size, ζ potential, morphology and proteomic profiles. While no significant differences in average EV size were observed between the two fractions, proteomic analysis revealed distinct quantitative and compositional variations. The 100k g fraction was enriched in proteins associated with cell periphery, plasma membrane, and extracellular region, whereas the 125k g fraction predominantly contained proteins from the extracellular region. Proteomic marker analysis confirmed that both fractions contained protein EV markers, such as transmembrane and transport proteins, soluble EV-associated proteins and proteins targeted to extracellular environment or cell wall. Conversely, negligible contamination from non-EV-related proteins was detected. Furthermore, transmission electron microscopy (TEM) confirmed that the fractions were devoid of non-vesicular extracellular nanoparticles (NVEPs), such as exomeres and supermeres. These findings demonstrate that coffee CSC represent a valuable and scalable platform for obtaining highly pure EVs, largely free from cellular membrane contamination, thus highlighting their significant potential for biotechnological applications.
HostingRepository	PRIDE
AnnounceDate	2026-02-16
AnnouncementXML	Submission_2026-02-15_16:22:48.355.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD071909
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Romina Belli
SpeciesList	scientific name: Coffea arabica (Arabian coffee); NCBI TaxID: NEWT:13443;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2025-12-12 05:54:18	ID requested
⏵ 1	2026-02-15 16:22:49	announced

10.3390/plants15030439;

10.6019/PXD071909;

Bonaventura AD, Scarpin D, Trotta G, Marchetti S, Petrussa E, Braidot E, Navarini L, Zancani M, L. Plants (Basel), 15(3):(2026) [pubmed]

submitter keyword: cell suspension cultures

Coffea arabica

extracellular vesicles (EVs)

morpho-34 metric traits

proteomics

unconventional protein secretion

Marco Zancani
contact affiliation	Dept. of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, 33100 Udine, Italy
contact email	marco.zancani@uniud.it
lab head
Romina Belli
contact affiliation	University of Trento
contact email	romina.belli@unitn.it
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/2026/02/PXD071909

PRIDE project URI

• PRIDE
  1. PXD071909
     1. Label: PRIDE project
     2. Name: Characterization of extracellular vesicles from cell suspension 2 cultures of Coffea arabica L.