PXD044666

PXD044666 is an original dataset announced via ProteomeXchange.

Title	Combining FAIMS based Glycoproteomic and DIA Proteomic of reveals widespread proteome alteration in response to changes in N. gonorrhoeae glycosylation.- FAIMS pglO alleles
Description	Protein glycosylation is increasingly recognized as a common protein modification across bacterial species. Within members of the Neisseria genus O-linked protein glycosylation plays important roles in virulence and antigenic variation yet our understanding of the substrates of glycosylation are limited. Recently it was identified that even closely related Neisserial species can possess O-oligosaccharyltransferases, pglOs, that possess varying glycosylation specificities suggesting that distinct targeting activities may impact both the glycoprotome as well as the proteome of Neisserial species. Within this work we explore this concept using of Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) fractionation and Data-Independent Acquisition (DIA) to allow the characterization of differences in the glycoproteomes and proteomes within N. gonorrhoeae strains expressing differing pglO alleles. We demonstrate the utility of FAIMS to expand the known glycoproteome of N. gonorrhoeae and enable comparative glycoproteomics of a recently reported panel of N. gonorrhoeae strains expressing different pglO allelic chimeras (15 pglO enzymes) with unique substrate targeting activities. Combining glycoproteomic insights with DIA proteomics we demonstrate that alterations within pglO alleles have widespread impacts on the proteome of N. gonorrhoeae yet lead to minimal effects on the abundance of glycoproteins. Additionally, while DIA analysis can allow occupancy to be inferred by the absence or presence of peptides known to be modified, we observe a poor correlation between DIA measurements of non-modified versions of glycopeptides and glycoproteomic analysis. Combined this work expands our understanding of the N. gonorrhoeae glycoproteome and supports that the expression of different pglO alleles appears to drive proteomic changes independent of the glycoproteins targeted for glycosylation.
HostingRepository	PRIDE
AnnounceDate	2024-02-01
AnnouncementXML	Submission_2024-02-01_05:17:49.241.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nichollas Scott
SpeciesList	scientific name: Neisseria gonorrhoeae MS11; NCBI TaxID: 528354;
ModificationList	complex glycosylation
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-08-20 07:13:04	ID requested
⏵ 1	2024-02-01 05:17:49	announced

Dataset with its publication pending

submitter keyword: FAIMS, DIA,Glycosylation, Neisseria gonorrhoeae, Post-translational modifications, Proteomics

Nichollas Scott
contact affiliation	Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
contact email	nichollas.scott@unimelb.edu.au
lab head
Nichollas Scott
contact affiliation	University of Melbourne
contact email	nichollas.scott@unimelb.edu.au
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD044666
     1. Label: PRIDE project
     2. Name: Combining FAIMS based Glycoproteomic and DIA Proteomic of reveals widespread proteome alteration in response to changes in N. gonorrhoeae glycosylation.- FAIMS pglO alleles