PXD070714-1

PXD070714 is an original dataset announced via ProteomeXchange.

Title	Evaluation of the Assembly Algorithm for De Novo Sequencing of Antibodies and Its Application in Analyzing Pan-Coronavirus Neutralizing Antibodies
Description	Humanized monoclonal antibodies, generated by grafting complementarity-determining regions (CDRs), offer significant advantages in terms of safety and efficacy as therapeutic agents. The accurate determination of heavy- and light-chain CDR sequences is crucial for the development and production of recombinant antibodies. In this study, we performed de novo sequencing on three humanized pan-coronavirus neutralizing antibodies (3D11, C1520, 5A6) utilizing an integrated SP-MEGD pretreatment method combined with a bottom-up mass spectrometry approach. The antibody sequences were reconstructed employing three assembly algorithms: PEAKS AB, Stitch, and Fusion. A systematic comparison was performed to assess the performance, specifically the coverage and accuracy of assembly, of these three algorithms. The results indicate that the Fusion algorithm achieves 100% coverage and accuracy under the current experimental conditions, for both light and heavy chains across all three antibodies while maintaining stability in high-variability regions of CDRs without introducing additional sequence insertions. In contrast, PEAKS AB and Stitch exhibited fragment missing, insertions, or misassembled segments in certain areas. In conclusion, the robust performance demonstrated by the Fusion algorithm provides a reliable foundation for sequence analysis that supports rational design and development efforts concerning pan-coronavirus neutralizing antibodies.
HostingRepository	iProX
AnnounceDate	2025-11-14
AnnouncementXML	Submission_2025-11-13_23:01:01.720.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yueting Xiong
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	deaminated residue; oxidation; methionine oxidation with neutral loss of 64 Da; methylated residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2025-11-13 23:00:37	ID requested
⏵ 1	2025-11-13 23:01:02	announced

Dataset with its publication pending

submitter keyword: Bottom-up mass spectrometry，De novo sequencing， Sequence assembly algorithms， Pan-coronavirus，Neutralizing antibodies

Ningshao Xia
contact affiliation	State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, National Institute for Data Science in Health and Medicine, Xiamen University
contact email	nsxia@xmu.edu.cn
lab head
Yueting Xiong
contact affiliation	State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, National Institute for Data Science in Health and Medicine, Xiamen University
contact email	ytxiong@xmu.edu.cn
dataset submitter

iProX dataset URI