PXD026795

PXD026795 is an original dataset announced via ProteomeXchange.

Title	Targeted Detection of SARS-CoV-2 Protein Variants by Mass Spectrometry
Description	COVID-19 vaccines are continuing to become more widely available, but accurate and rapid testing remains a crucial tool for slowing the spread of the SARS-CoV-2 virus. Although quantitative reverse transcription-polymerase chain reaction (qRT-PCR) remains the most prevalent testing methodology, numerous tests have been developed that are predicated on detection of the SARS-CoV-2 nucleocapsid protein, including liquid chromatography-tandem mass spectrometry (LC-MS/MS) and immunoassay based approaches. The continuing emergence of SARS-CoV-2 variants has complicated these approaches, as both qRT-PCR and antigen detection methods can be prone to missing viral variants. In this study, we describe a number of cases with COVID-19 where we were unable to detect the expected peptide targets from clinical nasopharyngeal swab samples that are typically identifiable in a targeted mass spectrometric assay. Whole genome sequencing revealed that single nucleotide polymorphisms in the gene encoding the viral nucleocapsid protein led to sequence variants that were not monitored in the targeted assay. Small modifications to the LC-MS/MS method ensured detection of the variants of the target peptide. Additional nucleocapsid variants were detected by performing bottom-up proteomic analysis of whole viral genome sequenced samples. This study demonstrates the importance of considering variants of SARS-CoV-2 in the assay design and highlights the flexibility of mass spectrometry-based approaches to detect variants as they evolve.
HostingRepository	PRIDE
AnnounceDate	2022-02-17
AnnouncementXML	Submission_2022-02-17_04:50:02.338.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; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2021-06-18 03:51:47	ID requested
⏵ 1	2022-02-17 04:50:03	announced

Maus A, Renuse S, Kemp J, Madugundu AK, Vanderboom PM, Blommel J, Jerde C, Dasari S, Kipp BR, Singh RJ, Grebe SK, Pandey A, Targeted Detection of SARS-CoV-2 Nucleocapsid Sequence Variants by Mass Spectrometric Analysis of Tryptic Peptides. J Proteome Res, 21(1):142-150(2022) [pubmed]

ProteomeXchange project tag: Covid-19

submitter keyword: Nucleocapsid, SARS-CoV-2, Single Amino Acid Protein Variants, Tandem Mass Spectrometry

Dr. Akhilesh Pandey
contact affiliation	Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
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

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/2022/02/PXD026795

PRIDE project URI

• PRIDE
  1. PXD026795
     1. Label: PRIDE project
     2. Name: Targeted Detection of SARS-CoV-2 Protein Variants by Mass Spectrometry