PXD074105

PXD074105 is an original dataset announced via ProteomeXchange.

Title	InstaNovo-P: A de novo peptide sequencing model for phosphoproteomics
Description	Phosphorylation, a crucial post-translational modification (PTM), plays a central role in cellular signaling and disease mechanisms. Mass spectrometry-based phosphoproteomics is widely used for system-wide characterization of phosphorylation events. However, traditional methods struggle with accurate phosphorylated site localization, complex search spaces, and detecting sequences outside the reference database. Advances in de novo peptide sequencing offer opportunities to address these limitations, but have yet to become integrated and adapted for phosphoproteomics datasets. Here, we present InstaNovo-P, a phosphorylation specific version of our transformer-based InstaNovo model, fine-tuned on extensive phosphoproteomics datasets. InstaNovo-P significantly surpasses existing methods in phosphorylated peptide detection and phosphorylated site localization accuracy across multiple datasets, including complex experimental scenarios. Our model robustly identifies peptides with single and multiple phosphorylated sites, effectively localizing phosphorylation events on serine, threonine, and tyrosine residues. We experimentally validate our model predictions by studying FGFR2 signaling, further demonstrating that InstaNovo-P uncovers phosphorylated sites previously missed by traditional database searches. These predictions align with critical biological processes, confirming the model’s capacity to yield valuable biological insights. InstaNovo-P adds value to phosphoproteomics experiments by effectively identifying biologically relevant phosphorylation events without prior information, providing a powerful analytical tool for the dissection of signaling pathways.
HostingRepository	PRIDE
AnnounceDate	2026-05-20
AnnouncementXML	Submission_2026-05-20_01:49:20.050.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Vahap Canbay
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	phosphorylated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2026-02-05 13:51:09	ID requested
⏵ 1	2026-05-20 01:49:20	announced

Dataset with its publication pending

submitter keyword: InstaNovo

De Novo Sequencing

Phosphoproteomics

Breast Cancer

FGFR2 signaling

Konstantinos Kalogeropoulos
contact affiliation	Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands Kavli Institute of Nanoscience, 2629 HZ Delft, Netherlands
contact email	konka@dtu.dk
lab head
Vahap Canbay
contact affiliation	Technical University of Denmark
contact email	vahcan@dtu.dk
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/PXD074105

PRIDE project URI

• PRIDE
  1. PXD074105
     1. Label: PRIDE project
     2. Name: InstaNovo-P: A de novo peptide sequencing model for phosphoproteomics