PXD046226-1

PXD046226 is an original dataset announced via ProteomeXchange.

Title	Site-specific glycoform analysis of human AGP and HL-60 cell lysate by the Glyco-RIDGE method using GRable Version 1.0
Description	High-throughput intact glycopeptide analysis is crucial for elucidating the physiological and pathological status of the glycans attached to each glycoprotein. Mass spectrometry-based glycoproteomic methods are challenging because of the diversity and heterogeneity of glycan structures. Therefore, we developed an MS1-based site-specific glycoform analysis method named "Glycan heterogeneity-based Relational IDentification of Glycopeptide signals on Elution profile (Glyco-RIDGE)" for a more comprehensive analysis. This method detects glycopeptide signals as a cluster based on the mass and chromatographic properties of glycopeptides and then searches for each combination of core peptides and glycan compositions by matching their mass and retention time differences. Here, we developed a novel browser-based software named GRable for semi-automated Glyco-RIDGE analysis with significant improvements in glycopeptide detection algorithms, including "parallel clustering." This unique function improved the comprehensiveness of glycopeptide detection and allowed the analysis to focus on specific glycan structures, such as pauci-mannose. The other notable improvement is evaluating the "confidence level" of the GRable results, especially using MS2 information. This function facilitated reduced misassignment of the core peptide and glycan composition and improved the interpretation of the results. Additional improved points of the algorithms are "correction function" for accurate monoisotopic peak picking; one-to-one correspondence of clusters and core peptides even for multiply sialylated glycopeptides; and "inter-cluster analysis" function for understanding the reason for detected but unmatched clusters. The significance of these improvements was demonstrated using purified and crude glycoprotein samples, showing that GRable allowed site-specific glycoform analysis of intact sialylated glycoproteins on a large-scale and in-depth. Therefore, this software will help us analyze the status and changes in glycans to obtain biological and clinical insights into protein glycosylation by complementing the comprehensiveness of MS2-based glycoproteomics. GRable can be freely run online using a web browser via the GlyCosmos Portal (https://glycosmos.org/grable).
HostingRepository	jPOST
AnnounceDate	2024-08-29
AnnouncementXML	Submission_2024-08-29_17:54:29.123.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Chiaki Nagai-Okatani
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	S-carboxamidomethyl-L-cysteine; unknown modification; unknown modification; L-methionine sulfoxide; unknown modification
Instrument	LTQ Orbitrap Velos; Orbitrap Fusion ETD

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-18 21:44:01	ID requested
⏵ 1	2024-08-29 17:54:29	announced

Nagai-Okatani C, Tominaga D, Tomioka A, Sakaue H, Goda N, Ko S, Kuno A, Kaji H, GRable Version 1.0: A Software Tool for Site-Specific Glycoform Analysis With Improved MS1-Based Glycopeptide Detection With Parallel Clustering and Confidence Evaluation With MS2 Information. Mol Cell Proteomics, 23(9):100833(2024) [pubmed]

submitter keyword: glycoproteomics, site-specific glycoform, glycan heterogeneity, software, AGP, HL-60

Chiaki Nagai-Okatani
lab head
Chiaki Nagai-Okatani
contact affiliation	National Institute of Advanced Industrial Science and Technology (AIST)
dataset submitter

jPOST dataset URI

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