Comparison of anti-peptide and anti-protein antibody-based purification techniques for detection of SARS-CoV-2 by targeted LC-MS/MS

•Detection of SARS-CoV-2 proteins from nasopharyngeal swabs using liquid chromatography-tandem mass spectrometry.•Direct comparison of anti-peptide and anti-protein antibody-based purification techniques.•Data showed that protein purification yielded greater signal intensity, but peptide purification yielded lower backgrounds and better specificity.•Using antibody purification techniques LC-MS/MS methods are capable of comparable sensitivity and specificity compared to reverse transcription-polymerase chain reaction.