PXD002803-1

PXD002803 is an original dataset announced via ProteomeXchange.

Title	Direct glycan structure determination of intact N-linked glycopeptides by low-energy collision-induced association tandem mass spectrometry and predicted spectral library searching
Description	Intact glycopeptide MS analysis to reveal site-specific protein glycosylation is an important frontier of proteomics. However, computational tools for analyzing MS/MS spectra of intact glycopeptides are still limited and not well-integrated into existing workflows. In this work, a novel computational tool which combines the spectral library building/searching tool, SpectraST (Lam et al. Nat. Methods 2008, 5, 873-875), and the glycopeptide fragmentation prediction tool, MassAnalyzer (Zhang et al. Anal. Chem. 2010, 82, 10194-10202) for intact glycopeptide analysis has been developed. Specifically, this tool enables the determination of the glycan structure directly from low-energy collision-induced dissociation (CID) spectra of intact glycopeptides. Given a list of possible glycopeptide sequences as input, a sample-specific spectral library of MassAnalyzer- predicted spectra is built using SpectraST. Glycan identification from CID spectra is achieved by spectral library searching against this library, in which both m/z and intensity information of the possible fragmentation ions are taken into consideration for improved accuracy. We validated our method using a standard glycoprotein, human transferrin, and evaluated its potential to be used in site-specific glycosylation profiling of glycoprotein datasets from LC/MS. For maximum usability, SpectraST is developed as part of the Trans-Proteomic Pipeline (TPP), a freely available and open-source software suite for MS data analysis
HostingRepository	PRIDE
AnnounceDate	2016-08-17
AnnouncementXML	Submission_2016-08-17_00:26:49.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yingwei Hu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	N-glycosylated residue
Instrument	LTQ

Revision	Datetime	Status	ChangeLog Entry
0	2015-08-27 02:30:32	ID requested
⏵ 1	2016-08-17 00:26:50	announced
2	2024-10-22 04:25:54	announced	2024-10-22: Updated project metadata.

Pai PJ, Hu Y, Lam H, Direct glycan structure determination of intact N-linked glycopeptides by low-energy collision-induced dissociation tandem mass spectrometry and predicted spectral library searching. Anal Chim Acta, 934():152-62(2016) [pubmed]

curator keyword: Technical, Biological

submitter keyword: Glycopeptide,LC-MSMS

Henry LAM
contact affiliation	The Hong Kong University of Science and Technology
contact email	kehlam@ust.hk
lab head
Yingwei Hu
contact affiliation	HKUST
contact email	husince@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD002803
     1. Label: PRIDE project
     2. Name: Direct glycan structure determination of intact N-linked glycopeptides by low-energy collision-induced association tandem mass spectrometry and predicted spectral library searching