PXD027425

PXD027425 is an original dataset announced via ProteomeXchange.

Title	Data-independent acquisition mass spectrometry for site-specific glycoproteomics characterization of SARS-CoV-2 spike protein
Description	The spike protein of SARS-CoV-2, the virus responsible for the global pandemic of COVID-19, is an abundant, heavily glycosylated surface protein that plays a key role in receptor binding and host cell fusion, and is the focus of all current vaccine development efforts. Variants of concern are now circulating worldwide that exhibit mutations in the spike protein. Protein sequence and glycosylation variations of the spike may affect viral fitness, antigenicity, and immune evasion. Global surveillance of the virus currently involves genome sequencing, but tracking emerging variants should include quantitative measurement of changes in site-specific glycosylation as well. In this work, we used data-dependent acquisition (DDA) and data-independent acquisition (DIA) mass spectrometry to quantitatively characterize the five N-linked glycosylation sites of the glycoprotein standard alpha-1-acid glycoprotein (AGP), as well as the 22 sites of SARS-CoV-2 spike protein. We found that DIA compared favorably to DDA in sensitivity, resulting in more assignments of low abundance glycopeptides. However, the reproducibility across replicates of DIA-identified glycopeptides was lower than that of DDA, possibly due to the difficulty of reliably assigning low abundance glycopeptides confidently. The differences in the data acquired between the two methods suggest that DIA out-performs DDA in terms of glycoprotein coverage but that overall performance is a balance of sensitivity, selectivity, and statistical confidence in glycoproteomics. We assert that these analytical and bioinformatics methods for assigning and quantifying glycoforms would benefit the process of tracking viral variants as well as for vaccine development.
HostingRepository	PRIDE
AnnounceDate	2022-02-12
AnnouncementXML	Submission_2022-02-11_18:51:17.755.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD027425
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Deborah Chang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-07-19 22:06:08	ID requested
⏵ 1	2022-02-11 18:51:18	announced

Dataset with its publication pending

ProteomeXchange project tag: Sars-cov-2, Covid-19

submitter keyword: glycosylation, DIA, glycoproteomics, SARS-CoV-2,mass spectrometry, spike protein

Joseph Zaia
contact affiliation	Boston University Medical Campus 670 Albany St., Rm. 509 Boston, MA 02118 USA
contact email	jzaia@bu.edu
lab head
Deborah Chang
contact affiliation	Boston University School of Medicine
contact email	changd@bu.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD027425
     1. Label: PRIDE project
     2. Name: Data-independent acquisition mass spectrometry for site-specific glycoproteomics characterization of SARS-CoV-2 spike protein