PXD018587-1

PXD018587 is an original dataset announced via ProteomeXchange.

Title	Open database searching enables the identification and comparison of glycoproteomes without defining glycan compositions prior to searching
Description	Mass spectrometry has become an indispensable tool for the characterisation of glycosylation across biological systems. Our ability to generate rich fragmentation data of glycopeptides has dramatically improved over the last decade yet our informatic approaches still lag be hide. This is especially true for the study of bacterial glycosylation where manual determination of glycopeptides is still heavily used. This dependence on manual assignment/identification is not scalable, extremely time consuming and limits accessibility of bacterial glycosylation studies to field specialists. As such computational approaches to examine bacterial glycosylation and determine glycan diversity within samples are desperately needed. Here we describe the use of wide-tolerance (up to 2000 Da) open searching as a means to rapidly examine bacterial glycoproteomes. We benchmarked this approach using N-linked glycopeptides of Campylobacter fetus subsp. fetus as well as O-linked glycopeptides of Acinetobacter baumannii and Burkholderia cenocepacia revealing glycopeptides modified with a range of glycans can be readily identified without defining the glycan masses prior to database searching. Utilising this approach, we demonstrate how wide tolerance searching can be used to compare glycan utilisation across bacterial species by examining the glycoproteomes of eight Burkholderia species (B. pseudomallei; B. multivorans; B. dolosa; B. humptydooensis; B. ubonensis, B. anthina; B. diffusa; B. pseudomultivorans). Finally, we also demonstrate how open searching enables the identification of low frequency glycoforms based on shared modified peptides sequences. Combined these results show that open searching is a robust computational approach for the determination of glycan diversity within novel microbial glycosylation systems.
HostingRepository	PRIDE
AnnounceDate	2020-06-24
AnnouncementXML	Submission_2020-06-23_22:41:59.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nichollas Scott
SpeciesList	scientific name: Burkholderia pseudomallei K96243; NCBI TaxID: 272560; scientific name: Burkholderia cenocepacia J2315; NCBI TaxID: 216591; scientific name: Acinetobacter baumannii; NCBI TaxID: 470; scientific name: Campylobacter fetus subsp. fetus; NCBI TaxID: 32019;
ModificationList	complex glycosylation
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-04-15 15:53:03	ID requested
⏵ 1	2020-06-23 22:41:59	announced
2	2024-10-22 05:07:40	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: Glycosylation, Post-translational modifications, Proteomics, wide tolerant database searching, Open searching, Glycopeptides, bacterial glycosylation, atypical glycosylation

Nichollas E. 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

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/2020/06/PXD018587

PRIDE project URI

• PRIDE
  1. PXD018587
     1. Label: PRIDE project
     2. Name: Open database searching enables the identification and comparison of glycoproteomes without defining glycan compositions prior to searching