PXD057496-1

PXD057496 is an original dataset announced via ProteomeXchange.

Title	Optimized Pipeline for Personalized Neurobiological Insights from Single Patient-Derived Neurospheres
Description	Quantitative proteomic approaches such as TMT labeling enable the amplification of biological material by combining multiple samples into a single analysis. This technique maximizes the data extracted from each sample and allows for precise comparative quantitative analysis between different experimental groups. In this study, we aimed to optimize the workflow for proteomic investigations using neurospheres derived from induced pluripotent stem cells (iPSCs). To improve both the efficiency and accuracy of our proteomic analysis, we compared different protocols and employed Tandem Mass Tag (TMT) labeling. Human neurospheres are three-dimensional, free-floating clusters primarily composed of neural progenitor cells, early-stage neurons, and radial glia. This diverse cell population more closely replicates the complexity of neural development compared to traditional 2D cultures, providing a more relevant model for studying neurogenesis, cell differentiation, and the underlying mechanisms of neurological diseases. Enhancing in vitro models through advanced cell culture techniques is crucial for reducing reliance on animal studies. In neural research, where access to human-relevant data is increasingly feasible, such improvements foster a deeper understanding of neural mechanisms and potential therapeutic targets. The use of 3D cultures represents a significant step forward in accurately modeling neural behavior and disease progression. By optimizing proteomic workflows and employing advanced labeling techniques, this study contributes to the development of more reliable and comprehensive in vitro neural models. This, in turn, supports the broader goal of advancing neural research while reducing reliance on animal models, leading to more ethical and potentially more accurate scientific outcomes that are clinically relevant to humans.
HostingRepository	PRIDE
AnnounceDate	2026-05-19
AnnouncementXML	Submission_2026-05-19_13:25:05.273.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Guillaume Nugue
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-04 10:07:21	ID requested
⏵ 1	2026-05-19 13:25:05	announced

10.1016/J.JPROT.2025.105576;

submitter keyword: TMT,IPCs, Neurosphere, LC-MS/MS

Magno Rodrigues Junqueira
contact affiliation	Laboratory of Translational Mass Spectrometry and Neuroproteomics, IQ-UFRJ
contact email	magnojunqueira@iq.ufrj.br
lab head
Guillaume Nugue
contact affiliation	UFRJ
contact email	nugueg@me.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/2026/05/PXD057496

PRIDE project URI

• PRIDE
  1. PXD057496
     1. Label: PRIDE project
     2. Name: Optimized Pipeline for Personalized Neurobiological Insights from Single Patient-Derived Neurospheres