PXD025414 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Extensive heterogeneity of glycopeptides in plasma revealed by deep glycoproteomic analysis |
Description | A number of plasma glycoproteins are clinically useful as biomarkers in a variety of diseases. Although thousands of proteins are present in plasma, >95% of the plasma proteome by mass is represented by only 22 proteins. This necessitates strategies to deplete the abundant proteins and enrich other subsets of proteins. Although glycoproteins are abundant in plasma, in routine proteomic analyses, glycopeptides are not often investigated. Traditional methods such as lectin-based enrichment of glycopeptides followed by deglycosylation have helped understand the glycoproteome, but they lack any information about the attached glycans. Here, we apply size-exclusion chromatography (SEC) as a simple strategy to enrich intact glycopeptides based on their larger size which achieves broad selectivity regardless of the nature of attached glycans. Using this approach, we identified 1,317 glycopeptides belonging to 266 glycosylation sites on 154 plasma glycoproteins. The deep coverage achieved by this approach was evidenced by extensive heterogeneity that was observed. For instance, 20-100 glycopeptides were observed per protein for the top 15 glycoproteins. Overall, we found 615 novel glycopeptides of which 39 glycosylation sites (from 38 glycoproteins) are not including in protein databases such as Uniprot and GlyconnectDB. We also identified 12 novel glycopeptides containing di-sialic acid, which is a rare glycan epitope. Thus, SEC allows for efficient LC-MS/MS-based deep glycoproteomics from low amounts (~1 l) of human plasma. Overall, the SEC-based method described here is a simple, rapid and high-throughput strategy for characterization of the glycoproteome. |
HostingRepository | PRIDE |
AnnounceDate | 2021-08-18 |
AnnouncementXML | Submission_2021-08-18_04:50:58.996.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Akhilesh Pandey |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue; deamidated residue |
Instrument | Q Exactive HF |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2021-04-15 01:42:27 | ID requested | |
⏵ 1 | 2021-08-18 04:50:59 | announced | |
Publication List
Saraswat M, Garapati K, Mun DG, Pandey A, Extensive heterogeneity of glycopeptides in plasma revealed by deep glycoproteomic analysis using size-exclusion chromatography. Mol Omics, 17(6):939-947(2021) [pubmed] |
Keyword List
submitter keyword: Plasma glycoproteomics, N-glycoproteomics, Size exclusion chromatography |
Contact List
Akhilesh Pandey |
contact affiliation | Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States |
contact email | pandey.akhilesh@mayo.edu |
lab head | |
Akhilesh Pandey |
contact affiliation | Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905 |
contact email | pandey.akhilesh@mayo.edu |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD025414
- Label: PRIDE project
- Name: Extensive heterogeneity of glycopeptides in plasma revealed by deep glycoproteomic analysis