PXD066160

PXD066160 is an original dataset announced via ProteomeXchange.

Title	Generalizable direct protein sequencing with InstaNexus
Description	Critical protein therapeutics, such as antibodies and nanobodies, are often not encoded in reference genomes, limiting their accurate characterization via standard proteomics. Current methods rely on indirect inference, fragmented outputs, and labor-intensive workflows, which hinder functional insights and routine application. Here, we present a generalizable, end-to-end workflow for direct protein sequencing, combining streamlined sample preparation, AI-driven de novo peptide sequencing, and tailored assembly to reconstruct contiguous protein sequences. A novel composite scoring framework prioritizes longer assemblies and coverage, enhancing accuracy and reducing ambiguity. Validation across diverse protein modalities demonstrates its utility and ability to robustly reconstruct functionally critical regions essential for optimizing therapeutic efficacy, stability, and immunogenicity. This workflow advances precision proteomics with promising applications in therapeutic discovery, immune profiling, and protein engineering.
HostingRepository	PRIDE
AnnounceDate	2026-02-23
AnnouncementXML	Submission_2026-02-23_03:31:47.292.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Konstantinos Kalogeropoulos
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; scientific name: Bos taurus (Bovine); NCBI TaxID: NEWT:9913;
ModificationList	acetylated residue; monohydroxylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2025-07-15 04:34:45	ID requested
⏵ 1	2026-02-23 03:31:47	announced

Dataset with its publication pending

submitter keyword: None

Konstantinos Kalogeropoulos
contact affiliation	Technical University of Denmark
contact email	konka@dtu.dk
lab head
Konstantinos Kalogeropoulos
contact affiliation	Technical University of Denmark
contact email	konskalogero@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/2026/02/PXD066160

PRIDE project URI

• PRIDE
  1. PXD066160
     1. Label: PRIDE project
     2. Name: Generalizable direct protein sequencing with InstaNexus