PXD025294-1

PXD025294 is an original dataset announced via ProteomeXchange.

Title	Targeted proteomics as a tool to detect SARS-CoV-2 proteins in clinical specimens
Description	The rapid, sensitive and specific detection of SARS-CoV-2 is critical in responding to the current COVID-19 outbreak. Here, we explore the potential of targeted mass spectrometry based proteomics for the detection of SARS-CoV-2 proteins in both research and clinical samples. First, we assessed the limit of detection for several SARS-CoV-2 proteins by parallel reaction monitoring (PRM) mass spectrometry. For Nucleocapsid the limit of detection was found to be in the mid-attomole range (0.9 x 10-12 g). Next, this PRM assay is applied to the detection of viral proteins in in vitro mucus substitutes, as well as in various clinical specimens such as nasopharyngeal swabs and sputum. In this proof-of-concept study SARS-CoV-2 proteins could unambiguously be detected in various clinical samples, suggesting that the sensitivity of this technology may be sufficiently high to further explore its potential role in diagnostics.
HostingRepository	PRIDE
AnnounceDate	2021-10-26
AnnouncementXML	Submission_2021-10-26_01:55:57.570.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jeroen Demmers
SpeciesList	scientific name: Cercopithecus aethiops (Green monkey) (Grivet); NCBI TaxID: 9534; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-04-09 03:43:08	ID requested
⏵ 1	2021-10-26 01:55:57	announced

Dataset with its publication pending

ProteomeXchange project tag: Covid-19

submitter keyword: SARS-CoV-2, COVID-19, Nucleocapsid protein (NP, NCAP), targeted mass spectrometry, parallel reaction monitoring, PRM, LC-MS, limit of detection, AQUA, clinical specimen

Jeroen Demmers
contact affiliation	Proteomics Center | Erasmus University Medical Center | Rotterdam, the Netherlands
contact email	j.demmers@erasmusmc.nl
lab head
Jeroen Demmers
contact affiliation	Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
contact email	j.demmers@erasmusmc.nl
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/2021/10/PXD025294

PRIDE project URI

• PRIDE
  1. PXD025294
     1. Label: PRIDE project
     2. Name: Targeted proteomics as a tool to detect SARS-CoV-2 proteins in clinical specimens