PXD021196 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Re-analysis of glycoproteomics data with MSFragger-Glyco |
Description | Reanalysis of submissions PXD011533 and PXD009476 using MSFragger-Glyco mode. Processed MSFragger results files (pepXML) and PSM tables (psm.tsv) supporting MSFragger-Glyco manuscript (Fast and Comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Recent advances in methods for enrichment and mass spectrometric analysis of intact glycopeptides have produced large-scale glycoproteomics datasets, but interpreting this data remains challenging. We present MSFragger-Glyco, aa new glycoproteomics mode of the MSFragger search engine, called MSFragger-Glyco, for fast and sensitive identification of N- and O-linked glycopeptides and open glycan searches. Reanalysis of recent N-glycoproteomics data resulted in annotation of 80% more glycopeptide-spectrum matches (glycoPSMs) than previously reported. In published O-glycoproteomics data, our method more than doubled the number of glycoPSMs annotated when searching the same glycans as the original search and yielded 4-6-fold increases when expanding searches to include additional glycan compositions and other modifications. Expanded searches also revealed many sulfated and complex glycans that remained hidden to the original search. |
HostingRepository | PRIDE |
AnnounceDate | 2020-10-06 |
AnnouncementXML | Submission_2020-10-05_23:02:27.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Daniel Polasky |
SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | glycosylated residue |
Instrument | Q Exactive HF; Orbitrap Fusion Lumos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2020-08-30 23:38:46 | ID requested | |
⏵ 1 | 2020-10-05 23:02:27 | announced | |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: glycoproteomics, glycan, glycopeptide, MSFragger, reanalysis, glycosylation, N-glycosylation, O-glycosylation |
Contact List
Alexey Nesvizhskii |
contact affiliation | Department of Pathology, University of Michigan Medical School |
contact email | nesvi@med.umich.edu |
lab head | |
Daniel Polasky |
contact affiliation | University of Michigan |
contact email | dpolasky@umich.edu |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD021196
- Label: PRIDE project
- Name: Re-analysis of glycoproteomics data with MSFragger-Glyco