PXD022550

PXD022550 is an original dataset announced via ProteomeXchange.

Title	Cov-MS: a community-based template assay for clinical MS-based protein detection in Sars-Cov-2 patients
Description	Rising population density and global mobility are among the reasons why pathogens such as SARS-CoV-2, the virus that causes COVID-19, spread so rapidly across the globe. The policy response to such pandemics will always have to include accurate monitoring of the spread, as this provides one of the few alternatives to total lockdown. However, COVID-19 diagnosis is currently performed almost exclusively by Reverse Transcription Polymerase Chain Reaction (RT-PCR). Although this is efficient, automatable and acceptably cheap, reliance on one type of technology comes with serious caveats, as illustrated by recurring reagent and test shortages. We, therefore, developed an alternative diagnostic test that detects proteolytically digested SARS-CoV-2 proteins using Mass Spectrometry (MS). We established the Cov-MS consortium, consisting of fifteen academic labs and several industrial partners to increase applicability, accessibility, sensitivity and robustness of this kind of Sars-Cov-2 detection. This in turn gave rise to the Cov-MS Digital Incubator that allows labs to join the effort, navigate and share their optimizations, and translate the assay into their clinic. As this test relies on viral proteins instead of RNA, it provides an orthogonal and complementary approach to RT-PCR, using other reagents that are relatively inexpensive and widely available, as well as orthogonally skilled personnel and different instruments.
HostingRepository	PRIDE
AnnounceDate	2022-02-14
AnnouncementXML	Submission_2022-02-14_02:22:14.951.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD022550
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Maarten Dhaenens
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: SARS Coronavirus CDC#200301157; NCBI TaxID: 292360;
ModificationList	monohydroxylated residue; deamidated residue
Instrument	TripleTOF 5600; TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2020-11-16 03:39:08	ID requested
1	2021-07-15 22:46:23	announced
⏵ 2	2022-02-14 02:22:15	announced	2022-02-14: Updated project metadata.

Van Puyvelde B, Van Uytfanghe K, Tytgat O, Van Oudenhove L, Gabriels R, Bouwmeester R, Daled S, Van Den Bossche T, Ramasamy P, Verhelst S, De Clerck L, Corveleyn L, Willems S, Debunne N, Wynendaele E, De Spiegeleer B, Judak P, Roels K, De Wilde L, Van Eenoo P, Reyns T, Cherlet M, Dumont E, Debyser G, t'Kindt R, Sandra K, Gupta S, Drouin N, Harms A, Hankemeier T, Jones DJL, Gupta P, Lane D, Lane CS, El Ouadi S, Vincendet JB, Morrice N, Oehrle S, Tanna N, Silvester S, Hannam S, Sigloch FC, Bhangu-Uhlmann A, Claereboudt J, Anderson NL, Razavi M, Degroeve S, Cuypers L, Stove C, Lagrou K, Martens GA, Deforce D, Martens L, Vissers JPC, Dhaenens M, Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients. JACS Au, 1(6):750-765(2021) [pubmed]

ProteomeXchange project tag: Covid-19, EPIC-XS

submitter keyword: SARS-COV2,Covid-19, DDA, Narrow-Window DIA

Maarten Dhaenens
contact affiliation	ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
contact email	maarten.dhaenens@ugent.be
lab head
Maarten Dhaenens
contact affiliation	Faculity of Pharmaceutical Biotechnology
contact email	maarten.dhaenens@ugent.be
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/2021/07/PXD022550

PRIDE project URI

• PRIDE
  1. PXD022550
     1. Label: PRIDE project
     2. Name: Cov-MS: a community-based template assay for clinical MS-based protein detection in Sars-Cov-2 patients