PXD020644-1

PXD020644 is an original dataset announced via ProteomeXchange.

Title	Development of mass spectrometry-based targeted assay for direct detection of novel SARS-CoV-2 coronavirus from clinical specimens
Description	The COVID-19 pandemic caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) has overwhelmed health systems worldwide and highlighted limitations of diagnostic testing. Several types of diagnostics including RT-PCR-based assays, antigen detection by lateral flow assays and antibody-based assays have been developed and deployed in a short time. However, many of these assays are lacking in sensitivity and/or specificity. Here, we describe an immunoaffinity purification followed by high resolution mass spectrometry-based targeted assay capable of detecting viral antigen in nasopharyngeal swab samples of SARS-CoV-2 infected individuals. Based on our discovery experiments using purified virus, recombinant viral protein and nasopharyngeal swab samples from COVID-19 positive patients, nucleocapsid protein was selected as a target antigen. We then developed anti-nucleocapsid antibody-based immunoprecipitation automated workflow followed by targeted field-asymmetric ion mobility mass spectrometry (FAIMS) - parallel reaction monitoring (PRM) assay using a preformed gradient liquid chromatography platform on an Orbitrap Exploris 480 mass spectrometer. An ensemble machine learning-based model for predicting COVID-19 positivity was created using fragment ion intensities in the PRM data. This resulted in 97.8% sensitivity and 100% specificity with RT-PCR-based molecular testing as the gold standard. Our results demonstrate that direct detection of infectious agents from clinical samples by mass spectrometry-based assays have potential to be deployed as diagnostic assays in clinical laboratories.
HostingRepository	PRIDE
AnnounceDate	2020-08-13
AnnouncementXML	Submission_2020-08-12_22:22:28.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 Eclipse; Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2020-07-29 22:10:51	ID requested
⏵ 1	2020-08-12 22:22:29	announced
2	2021-06-09 22:48:51	announced	2021-06-10: Updated project metadata.
3	2021-06-09 22:50:02	announced	2021-06-10: Updated project metadata.
4	2024-10-22 05:10:43	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

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

submitter keyword: Human, SARS-CoV-2, COVID19, Clinical diagnosis, LC-MSMS, Swab, Coronavirus, Viral antigen, SRM/PRM, Targeted proteomics, AP-MS

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/2020/08/PXD020644

PRIDE project URI

• PRIDE
  1. PXD020644
     1. Label: PRIDE project
     2. Name: Development of mass spectrometry-based targeted assay for direct detection of novel SARS-CoV-2 coronavirus from clinical specimens