PXD065680-1

PXD065680 is an original dataset announced via ProteomeXchange.

Title	Comparative Evaluation of Glycoproteomics Software for Rare Glycopeptide Identification
Description	Advancements in glycoproteomics software have improved glycopeptide identification; however, algorithm differences cause discrepancies in identified glycopeptide, even when identical datasets. We compared five state-of-the-art glycoproteomics software programs (Byonic, MSFragger-Glyco, pGlyco3, Glyco-Decipher, and GRable), investigating their unique capabilities, and examined their ability to identify rare sialic acid–containing glycopeptides (NeuGc and KDN) derived from BJAB-K20 cells, which lack UDP-N-acetylglucosamine 2-epimerase, the rate-limiting enzyme for sialic acid synthesis. Approximately half of the identified glycopeptides were unique to individual tools. Byonic identified the highest number of glycopeptides, whereas Glyco-Decipher and GRable identified complex highly branched glycan structures. NeuGc- and KDN-containing glycopeptides were identified by specific programs, highlighting their capability to handle rare glycan structures. To assess the reliability of these identifications, we reanalyzed the MS/MS spectra for the presence of diagnostic ions corresponding to each identified glycopeptide. Some software programs identified glycopeptides without detecting the corresponding diagnostic ions, raising concerns regarding result reliability. However, leveraging the distinct capabilities of each software enabled us to achieve a comprehensive and reliable analysis of glycopeptides, including those with rare glycan structures. Combining multiple glycoproteomics software programs with complementary strengths and incorporating post-verification steps, such as diagnostic ion analysis, enhance the accuracy and depth of glycopeptide identification.
HostingRepository	jPOST
AnnounceDate	2026-07-03
AnnouncementXML	Submission_2026-07-04_08:00:23.256.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Hiroaki Sakaue
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	S-carboxamidomethyl-L-cysteine; 2-pyrrolidone-5-carboxylic acid (Gln); L-methionine sulfoxide; Ammonia-loss; unknown modification
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2025-07-01 22:22:54	ID requested
⏵ 1	2026-07-04 08:00:23	announced

Dataset with its publication pending

submitter keyword: Glycoproteomics, BJAB-K20 cell

Hiroaki Sakaue
lab head
Hiroaki Sakaue
contact affiliation	National Institute of Advanced Industrial Science and Technology (AIST)
dataset submitter

jPOST dataset URI

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