PXD063526

PXD063526 is an original dataset announced via ProteomeXchange.

Title	De Novo Sequencing of Polyclonal Antibodies by Integrating Intact Mass, Top-Down and Bottom-Up Mass Spectrometry
Description	Antibodies are specialized proteins produced by the adaptive immune system to identify and neutralize harmful antigens. Antibody-based diagnostics and therapeutics have advanced rapidly, with recombinant antibodies derived from monoclonal antibodies (mAbs) becoming the preferred standard due to their high reproducibility and effectiveness. However, mAbs are limited to binding a single antigen epitope. Polyclonal antibodies (pAbs), on the other hand, are produced by multiple B cells and can target multiple epitopes, making them more robust against antigen variations. Despite their advantages, pAbs are notoriously challenging to sequence due to their high complexity. Current de novo sequencing methods based on mass spectrometry have shown limitations when applied to pAb mixtures, often requiring germline databases or yielding incomplete or inaccurate sequences. Here we propose PolySeq, a fully de novo sequencing workflow that integrates bottom-up, top-down, and intact mass spectrometry data to accurately sequence pAb samples without relying on external databases. Our workflow automates the entire sequencing process from peptides to full proteins, achieving complete and accurate antibody profiles. Evaluation results on a mixture of four known mAbs and a pAb sample derived from mouse myeloma demonstrate that our de novo antibody sequences achieved up to 100% coverage and accuracy, with strong supporting evidence from bottom-up, top-down, and intact mass data. Furthermore, antibodies recombinantly expressed using de novo sequencing results showed expected properties, such as binding affinity and antigen neutralization, thus confirming the accuracy and efficacy of our pAb de novo sequencing workflow.
HostingRepository	PRIDE
AnnounceDate	2025-10-31
AnnouncementXML	Submission_2025-10-31_01:26:01.109.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ngoc Hieu Tran
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monohydroxylated residue; deamidated residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-01 01:49:56	ID requested
⏵ 1	2025-10-31 01:26:01	announced

10.1016/J.MCPRO.2025.101088;

submitter keyword: intact mass, de novo sequencing, top-down, bottom-up,polyclonal antibody sequencing

Baozhen Shan
contact affiliation	Bioinformatics Solutions Inc., Waterloo, Ontario, Canada
contact email	bshan@bioinfor.com
lab head
Ngoc Hieu Tran
contact affiliation	Bioinformatics Solutions Inc.
contact email	htran@bioinfor.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/2025/10/PXD063526

PRIDE project URI

• PRIDE
  1. PXD063526
     1. Label: PRIDE project
     2. Name: De Novo Sequencing of Polyclonal Antibodies by Integrating Intact Mass, Top-Down and Bottom-Up Mass Spectrometry