The COVID-19 pandemic caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) has overwhelmed health systems worldwide and highlighted limitations of diagnostic testing. Several types of diagnostic tests including RT-PCR-based assays and antigen detection by lateral flow assays, each with their own strengths and weaknesses, have been developed and deployed in short time. Recent emergence of new SARS-CoV-2 variants has necessitated modification of current tests requiring additional test development efforts. Detection of viral antigen using liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a potential approach for detecting viral antigens and their variants. Here, we describe an immunoaffinity purification approach followed a by high resolution mass spectrometry-based targeted qualitative assay capable of detecting SARS-CoV-2 viral antigens and their variants from nasopharyngeal swab samples.