PXD021080

PXD021080 is an original dataset announced via ProteomeXchange.

Title	Development of a parallel reaction monitoring (PRM) mass spectrometry-assay for the detection of SARS-CoV-2 spike glycoprotein and nucleoprotein
Description	There is an urgent need for robust and high-throughput methods for SARS-CoV-2 detection in suspected pa-tient samples to facilitate disease management, surveillance, and control. Although nucleic acid detection methods such as RT-PCR are the gold standard, during the current pandemic the deployment of RT-PCR tests has been extremely slow, and key reagents such as PCR primers, and RNA extraction kits are at critical shortages. Rapid point-of-care viral antigen detec-tion methods have been previously employed for the diagnosis of respiratory viruses such as influenza and respiratory syn-cytial viruses. Therefore, the direct detection of SARS-CoV-2 viral antigens in patient samples could also be used for diagno-sis of active infection and alternative methodologies for specific and sensitive viral protein detection should be explored. Targeted mass spectrometry techniques have enabled the identification and quantitation of a defined subset of pro-teins/peptides at single amino acid resolution with attomole level sensitivity and high reproducibility. Herein we report a tar-geted mass spectrometry assay for the detection of SARS- CoV-2 spike protein and nucleoprotein in a relevant biologi-cal matrix. Recombinant full-length spike protein and nucleoprotein were digested and prototypic peptides were selected for parallel reaction monitoring (PRM) quantitation using a high resolution Orbitrap instrument. A spectral library, which con-tained 7 proteotypic peptides (4 from spike protein and 3 from nucleoprotein) and the top 3 to 4 transitionsMS2 spectra, was generated and evaluated. From the original spectral library, we selected 2 best performing peptides for the final PRM assay. The assay was evaluated using mock test samples containing inactivated SARS-CoV-2 virions, added to in-vitro de-rived mucus. The PRM assay provided a limit of detection (LOD) of ~200 attomoles and a limit of quantitation (LOQ) of ~ 390 attomoles. Extrapolating from the test samples, the projected titer of virus particles necessary for detection of SARS-CoV-2 spike and nucleoprotein detection was approximately 2E5 viral particles/mL, making it an attractive alternative to RT-PCR assays. Potentially mass spectrometry-based methods for viral antigen detection may deliver higher throughput and could serve as a complementary diagnostic tool to RT-PCR. Furthermore, this assay could be used to evaluate the pres-ence of SARS-CoV-2 in archived or recently collected biological fluids, in-vitro derived research materials, and wastewater samples
HostingRepository	PRIDE
AnnounceDate	2022-01-12
AnnouncementXML	Submission_2022-01-12_08:11:35.855.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Raghothama Chaerkady
SpeciesList	scientific name: SARS coronavirus WHU; NCBI TaxID: 247149;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-08-24 05:32:48	ID requested
⏵ 1	2022-01-12 08:11:36	announced

Cazares LH, Chaerkady R, Samuel Weng SH, Boo CC, Cimbro R, Hsu HE, Rajan S, Dall'Acqua W, Clarke L, Ren K, McTamney P, Kallewaard-LeLay N, Ghaedi M, Ikeda Y, Hess S, Development of a Parallel Reaction Monitoring Mass Spectrometry Assay for the Detection of SARS-CoV-2 Spike Glycoprotein and Nucleoprotein. Anal Chem, 92(20):13813-13821(2020) [pubmed]

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

submitter keyword: parallel reaction monitoring, SARS-CoV-2, heavy standard peptides, QExactive HF-X, Spike protein, nucleoprotein, skyline

Sonja Hess
contact affiliation	Sonja Hess, Dr. rer. nat. Director, Dynamic Omics AstraZeneca R&D Antibody Discovery and Protein Engineering One Medimmune Way, Gaithersburg, MD 20878
contact email	sonja.hess@astrazeneca.com
lab head
Raghothama Chaerkady
contact affiliation	MedImmune
contact email	chaerkadyr@medimmune.com
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/2022/01/PXD021080

PRIDE project URI

• PRIDE
  1. PXD021080
     1. Label: PRIDE project
     2. Name: Development of a parallel reaction monitoring (PRM) mass spectrometry-assay for the detection of SARS-CoV-2 spike glycoprotein and nucleoprotein