PXD058296-1

PXD058296 is an original dataset announced via ProteomeXchange.

Title	Spatially Resolved Protein Biomarkers of Thymus Compartmentalization Identified via Integrated MALDI Imaging and Proteomics
Description	The identification of spatially resolved proteomes has seen recent breakthroughs, yet challenges remain, particularly in combining protein identification with localization in a single experimental run. Matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) ad-dresses these limitations, allowing spatial mapping of proteins directly on tissue sections without the need for antibodies. This study introduces a novel approach to map protein changes in thym-ic tissue, particularly following chemotherapy treatment, by combining mass spectrometry imag-ing (MALDI-MSI) with liquid chromatography-mass spectrometry (LC-MS/MS). We developed a scoring system to match molecular signals from MALDI-MSI with proteomic data, allowing for precise identification of proteins involved in thymic function. Our results reveal key changes in protein expression, particularly in areas related to cell migration, cytoskeletal remodeling, and thymic regeneration. By analyzing the distribution of proteins like Keratin 8 (KRT8), Nucleoporin TPR, Cysteine- and Glycine-Rich Protein 3 (CSPR3), and Tubulin-Associated Chaperone-A (TBCA), we were able to observe shifts in thymic compartment architecture, highlighting the im-pact of chemotherapy on thymic tissue. This approach offers a new way to visualize and under-stand thymic remodeling and regeneration, with potential applications for monitoring chemother-apy effects and identifying biomarkers for monitoring thymic recovery.
HostingRepository	PRIDE
AnnounceDate	2025-10-30
AnnouncementXML	Submission_2025-10-29_17:47:08.071.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Simone Sidoli
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	2024-11-26 15:58:50	ID requested
⏵ 1	2025-10-29 17:47:08	announced

Dataset with its publication pending

submitter keyword: mass spectrometry, chemotherapy,imaging, thymus

Simone Sidoli
contact affiliation	Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 14061, United States
contact email	simone.sidoli@einsteinmed.edu
lab head
Simone Sidoli
contact affiliation	Albert Einstein College of Medicine
contact email	simone.sidoli@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/2025/10/PXD058296

PRIDE project URI

• PRIDE
  1. PXD058296
     1. Label: PRIDE project
     2. Name: Spatially Resolved Protein Biomarkers of Thymus Compartmentalization Identified via Integrated MALDI Imaging and Proteomics