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

Abstract

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 emergence of the pandemic. Mass spectrometry has been largely used in this regard. A critical part of mass spectrometric analyses is the proteome database required for the identification of peptides. Presently, the mutational information on proteins available on SARS-CoV-2 databases cannot be used to analyze data extracted from mass spectrometers. Hence, we developed the novel Mutant Peptide Database (MPD) for the mass spectrometry (MS)-based identification of mutated peptides, which contains information from 11 proteins of SARS-CoV-2 from a total of 21,549 SARS-CoV-2 variants across different regions of India. The database was validated using clinical samples, and its applicability was also demonstrated with the mutated peptides extracted from the literature. We believe that MPD will support broad-spectrum MS-based studies like viral detection, disease pathogenesis, and therapeutics with respect to SARS-CoV-2 and its variants.

Distinguishing common SARS-CoV2 omicron and recombinant variants with high resolution mass spectrometry

“…In particular, the role of high resolution mass spectrometry in the differentiation of SARS-CoV2 variants and sub-variants with high confidence 21,22 provide a broad framework for the implementation of a clinical analytic approach that offers benefits over lower resolution, low mass accuracy conventional MALDI-TOF or QTOF, and time and higher sample consuming LC-ESI-MS strategies 26 where liquid chromatographic separation and tandem MS/MS sequencing steps are necessary. 29 Even when so-called selective reaction monitoring (SRM) or multiple reaction monitoring (MRM) is employed, establishing precursor and fragment ion pairs that are efficiently produced and detected must be determined a priori, and the fragmentation (reaction) time and efficiency of peptide fragmentation remains a limitation. 30,31 The latter reduces the sensitivity of analysis over MS-only analyses, irrespective of the MS instrumentation deployed.…”

The 2023 Report on the Proteome from the HUPO Human Proteome Project

“…A herpesvirus infection primes the cell cycle state of neighboring cells to facilitate subsequent rounds of viral infection with the same virus or other nuclear-replicating viruses, while cells farther away from the site of infection displayed increased levels of immune factors . From continued work on the COVID-19 pandemic, databases were constructed for the MS identification of mutated peptides from SARS-CoV-2 variants across different geographical regions . A MALDI-ToF-MS method was optimized for the rapid detection of the SARS-CoV-2 nucleoprotein at a level of 8 amol/μL .…”

“…The U.S. National Cancer Institute’s Clinical Proteomics Tumor Analysis Consortium (CPTAC) and International Cancer Proteomics Consortium (ICPC) have set standards, established procedures, provided reagents, and populated massive data sets on more than a dozen major types of cancers (see Cancer B-D/HPP report). Proteomics has also advanced insights into COVID-19, ,, cardiovascular, , and neurological disorders, and diseases of the eye. New workflows are being developed for working with low-level ,,− and low-volume samples. , Network analysis continues to inform studies on disease-related pathways. − …”