PXD006031

PXD006031 is an original dataset announced via ProteomeXchange.

Title	A comprehensive, open-source platform for mass spectrometry based glycoproteomics data analysis
Description	Glycosylation is among the most abundant and diverse protein post-translational modifications (PTMs) identified to date. The structural analysis of this PTM is challenging due to the diverse monosaccharides which are not conserved among organisms, the branched nature of glycans, their isomeric structures, and heterogeneity in the glycan distribution at a given site. Glycoproteomics experiments have adopted the traditional high-throughput LC-MSn proteomics workflow to analyze site-specific glycosylation. However, comprehensive computational platforms for data analyses are scarce. To address this limitation, we present a comprehensive, open-source, modular software for glycoproteomics data analysis called GlycoPAT (GlycoProteomics Analysis Toolbox). The program introduces ‘SmallGlyPep’ as a minimal linear representation of glycopeptides for MSn data analysis. It enables MS/MS analysis of N- and O-linked glycosylation using a novel scoring scheme to rank the hits based on cross-correlation and probability based analysis. False discovery calculations, parallel computing facilities and user-friendly GUIs (Graphical User Interfaces) are also provided. GlycoPAT is used to analyze site-specific glycosylation on simple glycoproteins, protein mixtures and human plasma cryoprecipitate. The results show that the simultaneous consideration of peptide and glycan fragmentation enables high quality MS spectrum annotation in three common MS/MS fragmentation modes: CID, HCD and ETD.
HostingRepository	PRIDE
AnnounceDate	2017-09-19
AnnouncementXML	Submission_2019-02-12_08:16:48.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kai Cheng
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	complex glycosylation
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2017-03-06 03:54:07	ID requested
1	2017-09-19 05:00:28	announced
⏵ 2	2019-02-12 08:16:50	announced	Updated publication reference for PubMed record(s): 28887379.

Liu G, Cheng K, Lo CY, Li J, Qu J, Neelamegham S, A Comprehensive, Open-source Platform for Mass Spectrometry-based Glycoproteomics Data Analysis. Mol Cell Proteomics, 16(11):2032-2047(2017) [pubmed]

curator keyword: Technical

submitter keyword: Human, Plasma, LC-MS

Sriram Neelamegham
contact affiliation	Professor Department of Chemical & Biological Engineering, Biomedical Engineering and Clinical & Translational Research Center University at Buffalo State University of New York
contact email	neel@buffalo.edu
lab head
Kai Cheng
contact affiliation	University at Buffalo, SUNY
contact email	kaicheng@buffalo.edu
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/2017/09/PXD006031

PRIDE project URI

• PRIDE
  1. PXD006031
     1. Label: PRIDE project
     2. Name: A comprehensive, open-source platform for mass spectrometry based glycoproteomics data analysis