PXD018587 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 | 2024-10-22 |
AnnouncementXML | Submission_2024-10-22_05:07:39.848.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Nichollas Scott |
SpeciesList | scientific name: Burkholderia pseudomallei (strain 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 |
Dataset History
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. |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: wide tolerant database searching, bacterial glycosylation, Open searching,Glycosylation, Glycopeptides, Post-translational modifications, Proteomics, atypical glycosylation |
Contact List
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 | |
Full Dataset Link List
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 |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD018587
- Label: PRIDE project
- Name: Open database searching enables the identification and comparison of glycoproteomes without defining glycan compositions prior to searching