PXD033777

PXD033777 is an original dataset announced via ProteomeXchange.

Title	Proteotypic peptides for SARS-CoV-2 variant detection
Description	The recent SARS-CoV-2 omicron variant presented significant challenges to the global effort to counter the pandemic. SARS-CoV-2 is predicted to remain prevalent in the coming months, making the ability to identify SARS-CoV-2 variants imperative in understanding and controlling the pandemic. The predominant variant discovery method, genome sequencing, is time-consuming, insensitive, and expensive. Liquid chromatography-mass spectrometry (LC-MS) offers an exciting alternative detection modality provided that variant-containing peptide markers become well-established. This study demonstrates the potential to establish SARS-CoV-2 peptide markers by examining amino-acid variant-containing tryptic peptides, their MS fragmentation intensities, and their detection sensitivity in MS experiments. We have synthesized model tryptic peptides from of SARS-CoV-2 variants beta, gamma, delta, and omicron and evaluated their signal intensity, HCD spectra, and reverse phase retention time.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:32:01.656.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kantaphon Suddhapas
SpeciesList	scientific name: Severe acute respiratory syndrome coronavirus 2; NCBI TaxID: 2697049;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 240

Revision	Datetime	Status	ChangeLog Entry
0	2022-05-09 05:32:53	ID requested
1	2022-10-12 07:18:00	announced
2	2023-01-25 13:24:37	announced	2023-01-25: Updated project metadata.
⏵ 3	2023-11-14 08:32:02	announced	2023-11-14: Updated project metadata.

Suddhapas K, Choi MH, Shortreed MR, Timperman A, Evaluation of Variant-Specific Peptides for Detection of SARS-CoV-2 Variants of Concern. J Proteome Res, 21(10):2443-2452(2022) [pubmed]

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

submitter keyword: SARS-CoV-2,LCMS

Aaron Timperman
contact affiliation	University of Pennsylvania
contact email	atimperm@seas.upenn.edu
lab head
Kantaphon Suddhapas
contact affiliation	University of Pennsylvania
contact email	sudk@seas.upenn.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/10/PXD033777

PRIDE project URI

• PRIDE
  1. PXD033777
     1. Label: PRIDE project
     2. Name: Proteotypic peptides for SARS-CoV-2 variant detection