PXD018349-2

PXD018349 is an original dataset announced via ProteomeXchange.

Title	SugarQuant: a streamlined pipeline for multiplexed quantitative site-specific N-glycoproteomics
Description	Site-specific regulation of protein N-glycosylation is essential in human cells. However, accurate quantification of glycosylation sites and their individual glycan moieties in a cell-wide manner is still technically challenging. Here, we introduce SugarQuant, an integrated mass spectrometry-based pipeline comprising fast protein aggregation capture (PAC)-based sample preparation, optimized multi-notch MS3 LC-MS acquisition (Glyco-SPS-MS3) and a data-processing tool (GlycoBinder) that allows for confident, global identification and quantification of intact glycopeptides in complex biological samples. PAC greatly reduces the overall sample-handling time without compromising sensitivity. Glyco-SPS-MS3 combines high-resolution MS2 and MS3 scans, resulting in enhanced reporter signals of isobaric mass tags, improved detection of N-glycopeptide fragments, and significantly lowered interference in multiplexed quantification. GlycoBinder enables streamlined processing of Glyco-SPS-MS3 data, followed by a two-step database search which increases the identification rates of intact glycopeptides by up to 22% when compared with one-step database search strategies. SugarQuant was applied to identify and quantify more than 5,000 unique glycoforms in Burkitt’s lymphoma cells, and determined complex site-specific glycosylation changes that occurred upon inhibition of fucosylation at high confidence.
HostingRepository	PRIDE
AnnounceDate	2020-08-24
AnnouncementXML	Submission_2020-10-26_00:07:46.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Pan Fang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-04-03 03:15:42	ID requested
1	2020-08-24 04:08:28	announced
⏵ 2	2020-10-26 00:07:47	announced	2020-10-26: Updated publication reference for PubMed record(s): 33077710.

Fang P, Ji Y, Silbern I, Doebele C, Ninov M, Lenz C, Oellerich T, Pan KT, Urlaub H, A streamlined pipeline for multiplexed quantitative site-specific N-glycoproteomics. Nat Commun, 11(1):5268(2020) [pubmed]

submitter keyword: glycosylation

Kuan-Ting Pan
contact affiliation	max planck institute
contact email	kpan@mpibpc.mpg.de
lab head
Pan Fang
contact affiliation	Fudan University
contact email	pfang@mpibpc.mpg.de
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/2020/08/PXD018349

PRIDE project URI

• PRIDE
  1. PXD018349
     1. Label: PRIDE project
     2. Name: SugarQuant: a streamlined pipeline for multiplexed quantitative site-specific N-glycoproteomics