PXD063292-1

PXD063292 is an original dataset announced via ProteomeXchange.

Title	InstaNovo-P: A de novo peptide sequencing model for phosphoproteomics
Description	Phosphorylation, a vital 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 phosphosite localization, complex search spaces, and detecting sequences outside the reference database. Advances in denovo peptide sequencing offer opportunities to address these limitations, but have yet to be integrated and adapted for phosphoproteomics experiments. 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 phosphopeptide detection and phosphosite localization accuracy across multiple datasets, including complex experimental scenarios. Our model robustly identifies peptides with single and multiple phosphorylation sites, effectively localizing phosphorylation events on serine, threonine, and tyrosine residues. Experimental validation with FGFR2 signaling datasets further demonstrated that InstaNovo-P uncovers numerous phosphosites previously missed by traditional database searches, which 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	PanoramaPublic
AnnounceDate	2026-05-22
AnnouncementXML	Submission_2026-05-22_17:54:53.096.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	supported by repository but incomplete data and/or metadata
PrimarySubmitter	Vahap Canbay
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	Phospho; Oxidation; Label:13C(6)15N(2); Label:13C(6)15N(4)
Instrument	Orbitrap Eclipse; Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-24 09:56:48	ID requested
⏵ 1	2026-05-22 17:54:53	announced

no publication

submitter keyword: InstaNovo, De Novo Peptide Sequencing, Phosphoproteomics, Fibroblast Growth Factor Receptor 2 (FGFR2), Breast Cancer

Konstantinos Kalogeropoulos
contact affiliation	Technical University of Denmark
contact email	uadk@dtu.dk
lab head
Vahap Canbay
contact affiliation	Technical University of Denmark
contact email	vahcan@dtu.dk
dataset submitter

Panorama Public dataset URI