tetano
Editor, Senior Moderator
EBioMedicine
. 2021 Jul 3;69:103465.
doi: 10.1016/j.ebiom.2021.103465. Online ahead of print.
A mass spectrometry-based targeted assay for detection of SARS-CoV-2 antigen from clinical specimens
Santosh Renuse[SUP] 1 [/SUP], Patrick M Vanderboom[SUP] 2 [/SUP], Anthony D Maus[SUP] 2 [/SUP], Jennifer V Kemp[SUP] 2 [/SUP], Kari M Gurtner[SUP] 2 [/SUP], Anil K Madugundu[SUP] 3 [/SUP], Sandip Chavan[SUP] 2 [/SUP], Jane A Peterson[SUP] 4 [/SUP], Benjamin J Madden[SUP] 4 [/SUP], Kiran K Mangalaparthi[SUP] 5 [/SUP], Dong-Gi Mun[SUP] 2 [/SUP], Smrita Singh[SUP] 3 [/SUP], Benjamin R Kipp[SUP] 6 [/SUP], Surendra Dasari[SUP] 7 [/SUP], Ravinder J Singh[SUP] 8 [/SUP], Stefan K Grebe[SUP] 9 [/SUP], Akhilesh Pandey[SUP] 10 [/SUP]
Affiliations
Abstract
Background: 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 a short time.
Methods: 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 antigen from nasopharyngeal swab samples. Based on our discovery experiments using purified virus, recombinant viral protein and nasopharyngeal swab samples from COVID-19 positive patients, nucleocapsid protein was selected as a target antigen. We then developed an automated antibody capture-based workflow coupled to targeted high-field asymmetric waveform ion mobility spectrometry (FAIMS) - parallel reaction monitoring (PRM) assay on an Orbitrap Exploris 480 mass spectrometer. An ensemble machine learning-based model for determining COVID-19 positive samples was developed using fragment ion intensities from the PRM data.
Findings: The optimized targeted assay, which was used to analyze 88 positive and 88 negative nasopharyngeal swab samples for validation, resulted in 98% (95% CI = 0.922-0.997) (86/88) sensitivity and 100% (95% CI = 0.958-1.000) (88/88) specificity using RT-PCR-based molecular testing as the reference method.
Interpretation: Our results demonstrate that direct detection of infectious agents from clinical samples by tandem mass spectrometry-based assays have potential to be deployed as diagnostic assays in clinical laboratories, which has hitherto been limited to analysis of pure microbial cultures.
Keywords: COVID-19; Diagnostic assays; Ion mobility; Machine learning; Mass spectrometry; SARS-CoV-2.
. 2021 Jul 3;69:103465.
doi: 10.1016/j.ebiom.2021.103465. Online ahead of print.
A mass spectrometry-based targeted assay for detection of SARS-CoV-2 antigen from clinical specimens
Santosh Renuse[SUP] 1 [/SUP], Patrick M Vanderboom[SUP] 2 [/SUP], Anthony D Maus[SUP] 2 [/SUP], Jennifer V Kemp[SUP] 2 [/SUP], Kari M Gurtner[SUP] 2 [/SUP], Anil K Madugundu[SUP] 3 [/SUP], Sandip Chavan[SUP] 2 [/SUP], Jane A Peterson[SUP] 4 [/SUP], Benjamin J Madden[SUP] 4 [/SUP], Kiran K Mangalaparthi[SUP] 5 [/SUP], Dong-Gi Mun[SUP] 2 [/SUP], Smrita Singh[SUP] 3 [/SUP], Benjamin R Kipp[SUP] 6 [/SUP], Surendra Dasari[SUP] 7 [/SUP], Ravinder J Singh[SUP] 8 [/SUP], Stefan K Grebe[SUP] 9 [/SUP], Akhilesh Pandey[SUP] 10 [/SUP]
Affiliations
- PMID: 34229274
- DOI: 10.1016/j.ebiom.2021.103465
Abstract
Background: 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 a short time.
Methods: 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 antigen from nasopharyngeal swab samples. Based on our discovery experiments using purified virus, recombinant viral protein and nasopharyngeal swab samples from COVID-19 positive patients, nucleocapsid protein was selected as a target antigen. We then developed an automated antibody capture-based workflow coupled to targeted high-field asymmetric waveform ion mobility spectrometry (FAIMS) - parallel reaction monitoring (PRM) assay on an Orbitrap Exploris 480 mass spectrometer. An ensemble machine learning-based model for determining COVID-19 positive samples was developed using fragment ion intensities from the PRM data.
Findings: The optimized targeted assay, which was used to analyze 88 positive and 88 negative nasopharyngeal swab samples for validation, resulted in 98% (95% CI = 0.922-0.997) (86/88) sensitivity and 100% (95% CI = 0.958-1.000) (88/88) specificity using RT-PCR-based molecular testing as the reference method.
Interpretation: Our results demonstrate that direct detection of infectious agents from clinical samples by tandem mass spectrometry-based assays have potential to be deployed as diagnostic assays in clinical laboratories, which has hitherto been limited to analysis of pure microbial cultures.
Keywords: COVID-19; Diagnostic assays; Ion mobility; Machine learning; Mass spectrometry; SARS-CoV-2.