A SISCAPA-based approach for detection of SARS-CoV-2 viral antigens from clinical samples

Kiran K. Mangalaparthi, Sandip Chavan, Anil K. Madugundu, Santosh Renuse, Patrick M. Vanderboom, Anthony D. Maus, Jennifer Kemp, Benjamin R. Kipp, Stefan K. Grebe, Ravinder J. Singh, Akhilesh Pandey

Research output: Contribution to journalLetterpeer-review


SARS-CoV-2, a novel human coronavirus, has created a global disease burden infecting > 100 million humans in just over a year. RT-PCR is currently the predominant method of diagnosing this viral infection although a variety of tests to detect viral antigens have also been developed. In this study, we adopted a SISCAPA-based enrichment approach using anti-peptide antibodies generated against peptides from the nucleocapsid protein of SARS-CoV-2. We developed a targeted workflow in which nasopharyngeal swab samples were digested followed by enrichment of viral peptides using the anti-peptide antibodies and targeted parallel reaction monitoring (PRM) analysis using a high-resolution mass spectrometer. This workflow was applied to 41 RT-PCR-confirmed clinical SARS-CoV-2 positive nasopharyngeal swab samples and 30 negative samples. The workflow employed was highly specific as none of the target peptides were detected in negative samples. Further, the detected peptides showed a positive correlation with the viral loads as measured by RT-PCR Ct values. The SISCAPA-based platform described in the current study can serve as an alternative method for SARS-CoV-2 viral detection and can also be applied for detecting other microbial pathogens directly from clinical samples.

Original languageEnglish (US)
Article number25
JournalClinical Proteomics
Issue number1
StatePublished - Dec 2021


  • COVID-19
  • Mass spectrometry
  • Parallel reaction monitoring (PRM)
  • SARS-CoV-2

ASJC Scopus subject areas

  • Molecular Medicine
  • Molecular Biology
  • Clinical Biochemistry


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