PXD021388

PXD021388 is an original dataset announced via ProteomeXchange.

Title	Detection of SARS-CoV-2 in nasal swabs using MALDI-MS
Description	Detection of SARS-CoV-2 using RT–PCR and other advanced methods can achieve high accuracy. However, their application is limited in countries that lack sufficient resources to handle large-scale testing during the COVID-19 pandemic. Here, we describe a method to detect SARS-CoV-2 in nasal swabs using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and machine learning analysis. This approach uses equipment and expertise commonly found in clinical laboratories in developing countries. We obtained mass spectra from a total of 362 samples (211 SARS-CoV-2-positive and 151 negative by RT–PCR) without prior sample preparation from three different laboratories. We tested two feature selection methods and six machine learning approaches to identify the top performing analysis approaches and determine the accuracy of SARS-CoV-2 detection. The support vector machine model provided the highest accuracy (93.9%), with 7% false positives and 5% false negatives. Our results suggest that MALDI-MS and machine learning analysis can be used to reliably detect SARS-CoV-2 in nasal swab samples.
HostingRepository	PRIDE
AnnounceDate	2020-09-11
AnnouncementXML	Submission_2020-09-10_22:20:35.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Leonardo Santos
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	autoflex; microflex

Revision	Datetime	Status	ChangeLog Entry
0	2020-09-09 23:02:05	ID requested
⏵ 1	2020-09-10 22:20:35	announced

Nachtigall FM, Pereira A, Trofymchuk OS, Santos LS, Detection of SARS-CoV-2 in nasal swabs using MALDI-MS. Nat Biotechnol, 38(10):1168-1173(2020) [pubmed]

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

submitter keyword: SARS-Cov-2, COVID-19, MALDI-MS, Human

L. S. Santos
contact affiliation	Instituto de Química de Recursos Naturales, Universidad de Talca, Talca, Chile
contact email	lssantos@utalca.cl
lab head
Leonardo Santos
contact affiliation	Universidad de Talca
contact email	lsiltos@yahoo.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/2020/09/PXD021388

PRIDE project URI

• PRIDE
  1. PXD021388
     1. Label: PRIDE project
     2. Name: Detection of SARS-CoV-2 in nasal swabs using MALDI-MS