PXD024101-1

PXD024101 is an original dataset announced via ProteomeXchange.

Title	Community Evaluation of Glycoproteomics Informatics Solutions Reveals High-Performance Search Strategies for Glycopeptide Analysis
Description	Mass spectrometry-based glycoproteomics studies now routinely report thousands of intact glycopeptides. Diverse informatics solutions aiding the challenging glycopeptide identification process have recently appeared, but their strengths and weaknesses have not been established leaving a critical knowledge gap that prevents rapid progress in the field. This interlaboratory study comprising both expert users (13 teams) and developers (9 teams) of glycoproteomics software is the first to evaluate the relative performance of current informatics solutions for accurate and comprehensive N- and O-glycopeptide identification. Two LC-MS/MS datasets of intact glycopeptides from serum proteins were shared with all teams. The relative team performance for large-scale glycopeptide analysis was systematically established through 11 orthogonal performance tests based on the assigned spectra reported by each team. This study has found that a diversity of approaches exists for comprehensive glycopeptide data analysis, has demonstrated the team-to-team (vari)ability of identifying intact glycopeptides from shared datasets, and, importantly, has revealed several high-performance informatics solutions and search strategies that will be useful to improve the challenging glycoproteomics data analysis in the immediate future.
HostingRepository	PRIDE
AnnounceDate	2021-11-03
AnnouncementXML	Submission_2021-11-03_06:14:21.730.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Rebeca Sakuma
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetic acid derivatized residue; complex glycosylation
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-02-10 00:06:41	ID requested
⏵ 1	2021-11-03 06:14:22	announced

Dataset with its publication pending

ProteomeXchange project tag: Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project, Glycoproteomics (B/D-HPP)

submitter keyword: Glycoproteomics, glycopeptide, informatics, software, mass spectrometry, search engine

Morten Thaysen-Andersen
contact affiliation	Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, Australia
contact email	morten.andersen@mq.edu.au
lab head
Rebeca Sakuma
contact affiliation	University of Sao Paulo
contact email	rebecasakuma@gmail.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/2021/11/PXD024101

PRIDE project URI

• PRIDE
  1. PXD024101
     1. Label: PRIDE project
     2. Name: Community Evaluation of Glycoproteomics Informatics Solutions Reveals High-Performance Search Strategies for Glycopeptide Analysis