PXD033978-1

PXD033978 is an original dataset announced via ProteomeXchange.

Title	Charting the proteoform landscape of serum proteins in individual donors by high-resolution native mass spectrometry
Description	Most proteins in serum are glycosylated, with several annotated as biomarkers and thus diagnostically important and of interest for their role in disease. Most methods for analyzing serum glycoproteins have used either glycan release or glycopeptide centric mass spectrometry-based approaches, which provide excellent tools for analyzing known glycans, but neglect previously undefined or unknown glycosylation and/or other co-occurring modifications. High-resolution native mass spectrometry is a relatively new technique for the analysis of intact glycoproteins, providing a ‘what you see is what you get’ mass profile of a protein, allowing the qualitative and quantitative observation of all modifications present. So far, a disadvantage of this approach has been that it centers mostly on just one specific serum glycoprotein at the time. To address this issue, we introduce an IEX-based fractionation method capable of isolating and analyzing, in parallel, over 20 serum (glyco)proteins, covering a mass range between 30 and 190 kDa, from 150 µL of serum. The proteoform profiles of four selected proteins of interest, i.e., alpha-1-antitrypsin, ceruloplasmin, hemopexin and complement protein C3, are characterized and discussed in-depth. Our detailed analyses enabled the annotation of N- and O-glycans, protein cysteinylation, metal-ion binding, endogenous proteolysis and the detection of co-occurring genetic variants. Finally, we applied our approach to a small set of serum samples from healthy and diseased individuals. In these, we qualitatively and quantitatively monitored the changes in proteoform profiles of ceruloplasmin and reveal a substantial increase in fucosylation and glycan occupancy in patients with late-stage hepatocellular carcinoma and pancreatic cancer as compared to healthy donor samples.
HostingRepository	PRIDE
AnnounceDate	2022-09-06
AnnouncementXML	Submission_2022-09-06_10:46:23.145.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Dario Cramer
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	cysteinylation (disulfide with free L-cysteine); acetylated residue; formylated residue; monohydroxylated residue; complex glycosylation; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480; Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2022-05-18 07:39:35	ID requested
⏵ 1	2022-09-06 10:46:23	announced
2	2023-11-14 08:56:37	announced	2023-11-14: Updated project metadata.

10.1021/ACS.ANALCHEM.2C02215;

submitter keyword: serum, native ms, lc-msms, glycosylation, proteomics

Albert Heck
contact affiliation	Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Science, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, The Netherlands
contact email	a.j.r.heck@uu.nl
lab head
Dario Cramer
contact affiliation	Utrecht University
contact email	d.a.t.cramer@uu.nl
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/2022/09/PXD033978

PRIDE project URI

• PRIDE
  1. PXD033978
     1. Label: PRIDE project
     2. Name: Charting the proteoform landscape of serum proteins in individual donors by high-resolution native mass spectrometry