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PXD033978

PXD033978 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleCharting the proteoform landscape of serum proteins in individual donors by high-resolution native mass spectrometry
DescriptionMost 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. 
HostingRepositoryPRIDE
AnnounceDate2023-11-14
AnnouncementXMLSubmission_2023-11-14_08:56:36.963.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterDario Cramer
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListcysteinylation (disulfide with free L-cysteine); acetylated residue; monohydroxylated residue; formylated residue; complex glycosylation; iodoacetamide derivatized residue
InstrumentOrbitrap Exploris 480; Q Exactive Plus
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-05-18 07:39:35ID requested
12022-09-06 10:46:23announced
22023-11-14 08:56:37announced2023-11-14: Updated project metadata.
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: glycosylation, lc-msms, proteomics, native ms,serum
Contact List
Albert Heck
contact affiliationBiomolecular 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 emaila.j.r.heck@uu.nl
lab head
Dario Cramer
contact affiliationUtrecht University
contact emaild.a.t.cramer@uu.nl
dataset submitter
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Dataset FTP location
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