PXD029700

PXD029700 is an original dataset announced via ProteomeXchange.

Title	Improving statistical certainty of glycosylation similarity between influenza A virus variants using data-independent acquisition mass spectrometry
Description	The amino acid sequences of immunodominant domains of hemagglutinin (HA) on the surface of influenza A virus (IAV) evolve rapidly, producing viral variants. HA mediates receptor recognition, binding and cell entry, and serves as the target for IAV vaccines. Glycosylation, a post-translational modification that places large, branched polysaccharide molecules on proteins, can modulate the function of HA, and can shield antigenic regions allowing for viral evasion from immune responses. Our previous work showed that subtle changes in the HA protein sequence can have a measurable change in glycosylation. Thus, being able to measure quantitatively how glycosylation changes in viral variants is critical for understanding how HA function may change throughout viral evolution. Moreover, understanding quantitatively how the choice of viral expression systems affects glycosylation can help in the process of vaccine design and manufacture. Although IAV vaccines are most commonly expressed in chicken eggs, cell-based vaccines have many advantages and the adoption of more cell-based vaccines would be an important step in mitigating seasonal influenza and protecting against future pandemics. Here, we have investigated the use of data-independent acquisition (DIA) mass spectrometry for quantitative glycoproteomics. We found that DIA improved the sensitivity of glycopeptide detection for four variants of A/Switzerland/9715293/2013 IAV: WT and mutant, each expressed in chicken eggs and MDCK cells. We used the Tanimoto similarity metric to quantify changes in glycosylation between WT and mutant, and between egg-expressed and cell-expressed virus. Our DIA site-specific glycosylation similarity comparison of WT and mutant expressed in eggs confirmed our previous analysis while achieving greater depth of coverage. We found that sequence changes resulting from different viral expression systems affected distinct glycosylation sites of HA. Our methods can be applied to track glycosylation changes in circulating IAV variants to bolster the genomic surveillance already being done, for a more complete understanding of IAV evolution.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:57:20.743.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD029700
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Deborah Chang
SpeciesList	scientific name: Gallus gallus (Chicken); NCBI TaxID: 9031; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Canis familiaris (Dog) (Canis lupus familiaris); NCBI TaxID: 9615;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-11-12 06:06:04	ID requested
1	2022-09-24 17:02:19	announced
⏵ 2	2023-11-14 08:57:21	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: influenza, DIA, glycoproteomics,mass spectrometry, glycosylation similarity, hemagglutinin

Joseph Zaia
contact affiliation	Boston University School of Medicine
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. PXD029700
     1. Label: PRIDE project
     2. Name: Improving statistical certainty of glycosylation similarity between influenza A virus variants using data-independent acquisition mass spectrometry