PXD062479-1

PXD062479 is an original dataset announced via ProteomeXchange.

Title	Mapping the Toxoplasma gondii cytosolic interactome by crosslinking mass spectrometry and machine learning
Description	Protein–protein interactions (PPIs) are fundamental to cellular processes and pathogen biology, yet remain undercharacterized in the human parasite Toxoplasma gondii. Here, we apply crosslinking mass spectrometry (XL-MS) to map the cytosolic interactome of T. gondii tachyzoites at proteome scale. Using an optimized workflow that combines MS-cleavable and non-cleavable crosslinker searches, we identified 391 PPIs and over 5,000 residue-residue contacts, including known complexes such as the ribosome and proteasome, as well as novel interactions among dense granule proteins. Structural mapping confirmed the spatial plausibility of crosslinks, while detection of homo-dimers and transient interactions highlighted the sensitivity of our approach. We further employed machine learning using LightGBM to rescue lower-confidence interactions by integrating large-scale biological data including gene expression, subcellular localization, and known functional associations. The model achieved 98.7% accuracy and enabled expanded interactome reconstruction. This study establishes XL-MS as a powerful tool for characterizing PPIs in parasites and provides a foundational interactome for T. gondii, with implications for understanding parasite biology and host-pathogen interactions.
HostingRepository	PRIDE
AnnounceDate	2025-07-26
AnnouncementXML	Submission_2025-07-26_05:56:49.888.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Simone Sidoli
SpeciesList	scientific name: Toxoplasma gondii type I; NCBI TaxID: 1209525;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-01 13:39:12	ID requested
⏵ 1	2025-07-26 05:56:50	announced

Dataset with its publication pending

submitter keyword: machine learning, cytosol, protein–protein interactions, dense granule proteins, crosslinking mass spectrometry, interactome, DSBSO, host-pathogen interactions, structural mapping,Toxoplasma gondii, LightGBM, parasite proteomics, ribosome, proteasome

Simone Sidoli
contact affiliation	Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, 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/2025/07/PXD062479

PRIDE project URI

• PRIDE
  1. PXD062479
     1. Label: PRIDE project
     2. Name: Mapping the Toxoplasma gondii cytosolic interactome by crosslinking mass spectrometry and machine learning