PXD058411-1

PXD058411 is an original dataset announced via ProteomeXchange.

Title	The role of apoplastic fluid in driven somatic embryogenesis efficiency in olive – establishment of an efficient workflow for proteome and metabolome analysis
Description	Somatic embryogenesis (SE) is a process involving the formation of structures like the zygotic embryos, arising from the dedifferentiation of somatic cells without requiring fertilization. This process is routinely used for clonal propagation and genetic transformation in plants, but not for olive (Olea europaea sp. europaea) adult tissues due to their recalcitrant nature. An important but underexplored factor affecting olive SE is the release of organic bioactive molecules by embryogenic cultures into the culture medium (conditioned medium, CM). Secreted biomolecules, including proteins and metabolites, are involved in several essential biological processes, playing an important role in cellular communication, therefore, it is hypothesized that they could influence olive somatic embryogenic competence. To test this hypothesis, an new protocol was optimized for the analysis of CM from embryogenic lines derived from zygotic embryos and propagated through cyclic embryogenesis using liquid cultures. The optimized workflow is a multi-omics high-throughput platform, allowing the study of CM proteins and metabolites. Secreted proteins were initially separated from metabolites through filtration and protein extraction efficiency by employing lyophilization as a concentration step, followed by protein precipitation through three different protocols, were then evaluated by SDS-PAGE. LC-MS/MS was used to investigate the secretome composition. In turn, metabolite fraction was analysed through a 1H NMR spectroscopy platform, which allow to assess changes in the metabolite profile by comparing CM with control medium (ECO medium). These results underscore the high potential of the established workflow in identifying a wide range of proteins and metabolites, offering a valuable tool for further investigate the molecular factors influencing SE competence, contributing to future advancements in olive SE efficiency and regeneration.
HostingRepository	PRIDE
AnnounceDate	2025-11-01
AnnouncementXML	Submission_2025-11-01_11:16:56.723.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD058411
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Fátima Santos
SpeciesList	scientific name: Olea europaea subsp. europaea; NCBI TaxID: NEWT:158383;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 240

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-29 05:29:50	ID requested
⏵ 1	2025-11-01 11:16:57	announced

10.3390/HORTICULTURAE11030331;

10.6019/PXD058411;

submitter keyword: Somatic embryogenesis

olive

conditioned medium

proteome

metabolome

Hélia Cristina Guerra Cardoso
contact affiliation	MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, School of Science and Technology, University of Évora, Pólo da Mitra, Ap. 94, 7002-554 Évora, Portugal
contact email	hcardoso@uevora.pt
lab head
Fátima Santos
contact affiliation	IIS-FJD, UAM
contact email	ftxsantos@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/2025/11/PXD058411

PRIDE project URI

• PRIDE
  1. PXD058411
     1. Label: PRIDE project
     2. Name: The role of apoplastic fluid in driven somatic embryogenesis efficiency in olive – establishment of an efficient workflow for proteome and metabolome analysis