PXD057705

PXD057705 is an original dataset announced via ProteomeXchange.

Title	Prosit-XL: enhanced cross-linked peptide identification by accurate fragment intensity prediction to study protein-protein interactions and protein structures
Description	It has been shown that integrating peptide property predictions such as fragment intensity into the scoring process of peptide spectrum match can greatly increase the number of confidently identified peptides compared to using traditional scoring methods. Here, we introduce Prosit-XL, a robust and accurate fragment intensity predictor covering the cleavable (DSSO/DSBU) and non-cleavable cross-linkers (DSS/BS3), achieving high accuracy on various holdout sets with consistent performance on external datasets without fine-tuning. Due to the complex nature of false positives in XL-MS, a novel approach to data-driven rescoring was developed that benefits from Prosit-XL’s predictions while limiting the overestimation of the false discovery rate (FDR). We first evaluated this approach using two ground truth datasets (PXD029252, PXD042173) that demonstrate the accurate and precise FDR estimation. Second, we applied Prosit-XL on a proteome-scale dataset (JPST000845, PXD017711), demonstrating an up to ~3.4-fold improvement in PPI discovery compared to classic approaches. Finally, Prosit-XL was used to increase the coverage and depth of a spatially resolved interactome map of intact human cytomegalovirus virions (PXD031911), leading to the discovery of previously unobserved interactions between human and cytomegalovirus proteins.
HostingRepository	PRIDE
AnnounceDate	2025-05-18
AnnouncementXML	Submission_2025-05-18_12:37:38.375.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mostafa Kalhor
SpeciesList	scientific name: Cytomegalovirus; NCBI TaxID: 10358; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-10 06:56:21	ID requested
⏵ 1	2025-05-18 12:37:38	announced

Dataset with its publication pending

submitter keyword: Deep learning,Crosslinking mass spectrometry

Mathias Wilhelm
contact affiliation	Computational Mass Spectrometry, Technical University of Munich (TUM), Freising, Germany
contact email	matthias.wilhelm@tum.de
lab head
Mostafa Kalhor
contact affiliation	Technical University of Munich
contact email	mostafa.kalhor@tum.de
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/2025/05/PXD057705

PRIDE project URI

• PRIDE
  1. PXD057705
     1. Label: PRIDE project
     2. Name: Prosit-XL: enhanced cross-linked peptide identification by accurate fragment intensity prediction to study protein-protein interactions and protein structures