PXD021581

PXD021581 is an original dataset announced via ProteomeXchange.

Title	Prognostic accuracy of Mass Spectrometric Analysis of Plasma in COVID-19
Description	SARS-CoV-2 infection poses a worldwide public health problem affecting millions of people worldwide. There is a critical need for improvements in the noninvasive prognosis of COVID-19. We hypothesized that matrix-assisted laser desorption ionization mass spectrometry (MALDI-TOF MS) analysis combined with molecular-weight directed bottom-up proteomic analysis of plasma proteins may predict high and low risk cases of COVID-19. Patients and Methods: We used MALDI MS to analyze plasma small proteins and peptides isolated using C18 micro-columns from a cohort containing a total of 117 cases of high and low risk cases split into training (n = 88) and validation sets (n= 29). The plasma protein/peptide fingerprint obtained was used to train the algorithm before validation using a blinded test cohort. Several sample preparation, MS and data analysis parameters were optimized to achieve an overall accuracy of 85%, a sensitivity of 90%, and a specificity of 81% in the training set. In the blinded test set, this signature reached an overall accuracy of 93.1%, a sensitivity of 87.5%, and a specificity of 100%. From this signature, we identified two distinct regions corresponding to the single and doubly protonated proteins in the MALDI-TOF profile belonging to the same proteoforms. A combination of 1D SDS-PAGE and quantitative bottom-up proteomic analysis allowed the identification of intact and truncated forms of serum amyloid A-1 and A-2 proteins. We found a plasma proteomic profile that discriminates against patients with high and low risk COVID-19. Proteomic analysis of C18-fractionated plasma may have a role in the noninvasive prognosis of COVID-19. Further validation will be important to consolidate its clinical utility.
HostingRepository	PRIDE
AnnounceDate	2021-06-22
AnnouncementXML	Submission_2021-06-21_22:41:19.378.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Giuseppe Palmisano
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2020-09-21 00:07:08	ID requested
⏵ 1	2021-06-21 22:41:19	announced

Dataset with its publication pending

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

submitter keyword: COVID-19, SARS-CoV-2, Mass spectrometry, Biomarker, Plasma, Prognosis

Giuseppe Palmisano
contact affiliation	Glycoproteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, Brazil Av. Prof. Lineu Prestes, 1374 05508-900 - São Paulo – SP - Brazil Tel: + 55-11-99920-8662 palmisano.gp@gmail.com palmisano.gp@usp.br
contact email	palmisano.gp@gmail.com
lab head
Giuseppe Palmisano
contact affiliation	University of Sao Paulo
contact email	palmisano.gp@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD021581
     1. Label: PRIDE project
     2. Name: Prognostic accuracy of Mass Spectrometric Analysis of Plasma in COVID-19