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Detection of mutated peptides of SARS-CoV-2 from COVID-19-infected patients

ABSTRACT: This project involves the identification of mutated peptides from swab and plasma samples using an in-house developed Mutant Peptide Database (MPD)

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Plasma

SUBMITTER: Abhilash Barpanda

LAB HEAD: Sanjeeva Srivastava

PROVIDER: PXD029300 | Pride | 2023-05-10

REPOSITORIES: Pride

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			Action	DRS
	COVID_SWAB_2021_S112.raw	Raw
	COVID_SWAB_2021_S113.raw	Raw
	COVID_SWAB_2021_S114.raw	Raw
	COVID_SWAB_2021_S21.raw	Raw
	COVID_SWAB_2021_S22.raw	Raw

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Publications

Detection of Mutant Peptides of SARS-CoV-2 Variants by LC/MS in the DDA Approach Using an In-House Database.

Rajoria Sakshi S Halder Ankit A Tarnekar Ishita I Pal Pracheta P Bansal Prakhar P Srivastava Sanjeeva S

Journal of proteome research 20230424 6

Equipped with a dramatically high mutation rate, which happens to be a signature of RNA viruses, SARS-CoV-2 trampled across the globe infecting individuals of all ages and ethnicities. As the variants of concern (VOC) loomed large, definitive detection of SARS-CoV-2 strains became a matter of utmost importance in epidemiological and clinical research. Besides, unveiling the disease pathogenesis at the molecular level and deciphering the therapeutic targets became key priorities since the emergen ...[more]

PMID: 37093804

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2021-02-09 | PXD020580 | Pride

Proteomic Investigation Reveals Dominant Alterations of Neutrophil Degranulation and mRNA Translation Pathways in COVID-19 Patients

Project description:The altered molecular proteins and pathways in response to COVID-19 infection are still unclear. Here, we performed a comprehensive proteomics-based investigation of of nasopharyngeal swab samples from COVID-19 patients to identify viral and host peptides by employing simple extraction strategies and also established a panel of host proteins using high-resolution mass spectrometry. The differentially expressed peptides/proteins identified from host and pathogen correlated with the viral load of the host which indicates that these proteins might be good prognostic biomarkers of severity prediction. A few host proteins such as Interleukin-6, L-lactate dehydrogenase, C-reactive protein, Ferritin and Aspartate aminotransferase was found to be upregulated in COVID-19 positive patients using targeted MRM study. Further, the proteins L-lactate dehydrogenase, Aspartate aminotransferase and Alanine aminotransferase was also validated in the clinical settings using immunological assays. We also identified neutrophil degranulation, platelet degranulation, interleukin-12 signaling pathways, mRNA translation of proteins and , co-factor metabolomic process protein metabolism, and stress responses to be key GO enriched pathways, thus altered in the COVID-19 infected patients.providing the detailed investigation of host response in COVID-19 infection , thus providing the landscape of COVID-19 pathophysiology. This study thus also revealed that mass spectrometry-based detected host proteins/peptides has a potential for clinical translation and a few proteins might be routinely monitored in clinics for the disease progression, peptide tests can be used by clinicians for diagnosis as well as identified pathways/ markers as the predictors of disease progression. Furthermore, the identified proteins and their drug binding studies might aid in COVID-19 therapeutic interventions.

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