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PXD018349 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleSugarQuant: a streamlined pipeline for multiplexed quantitative site-specific N-glycoproteomics
DescriptionSite-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.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterPan Fang
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListTMT6plex-126 reporter+balance reagent acylated residue
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-04-03 03:15:42ID requested
12020-08-24 04:08:28announced
22020-10-26 00:07:47announced2020-10-26: Updated publication reference for PubMed record(s): 33077710.
Publication List
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]
Keyword List
submitter keyword: glycosylation
Contact List
Kuan-Ting Pan
contact affiliationmax planck institute
contact emailkpan@mpibpc.mpg.de
lab head
Pan Fang
contact affiliationFudan University
contact emailpfang@mpibpc.mpg.de
dataset submitter
Full Dataset Link List
Dataset FTP location
PRIDE project URI
Repository Record List
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