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. 2023 Jul 1;20(1):26.
doi: 10.1186/s12014-023-09415-y.

Development of a rapid and specific MALDI-TOF mass spectrometric assay for SARS-CoV-2 detection

Lydia Kollhoff  1   2 , Marc Kipping  1   2 , Manfred Rauh  3 , Uta Ceglarek  4 , Günes Barka  5 , Frederik Barka  5 , Andrea Sinz  6   7
Affiliations

Development of a rapid and specific MALDI-TOF mass spectrometric assay for SARS-CoV-2 detection

Lydia Kollhoff et al. Clin Proteomics. .

Abstract

We have developed a rapid and highly specific assay for detecting and monitoring SARS-CoV-2 infections by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). As MALDI-TOF mass spectrometers are available in a clinical setting, our assay has the potential to serve as alternative to the commonly used reverse transcriptase quantitative polymerase chain reaction (RT-qPCR). Sample preparation prior to MALDI-TOF-MS involves the tryptic digestion of SARS-CoV-2 proteins, followed by an enrichment of virus-specific peptides from SARS-CoV-2 nucleoprotein via magnetic antibody beads. Our MALDI-TOF-MS method allows the detection of SARS-CoV-2 nucleoprotein in sample collection medium as low as 8 amol/µl. MALDI-TOF mass spectra are obtained in just a few seconds, which makes our MS-based assay suitable for a high-throughput screening of SARS-CoV-2 in healthcare facilities in addition to PCR. Due to the specific detection of virus peptides, different SARS-CoV-2 variants are readily distinguished from each other. Specifically, we show that our MALDI-TOF-MS assay discriminates SARS-CoV-2 strain B.1.617.2 "delta variant" from all other variants in patients' samples, making our method highly valuable to monitor the emergence of new virus variants.

Keywords: COVID-19; MALDI; Mass spectrometry; SARS-COV-2.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Analytical Workflow of MALDI-TOF-MS Assay for SARS-CoV-2 Detection. The method is based on a specific detection of peptides derived from SARS-CoV-2 nucleoprotein. Nasopharyngeal swabs are collected and the medium is loaded on a 300-kDa molecular weight cut-off filter. After enzymatic proteolysis, specific peptides of SARS-CoV-2 nucleoprotein are enriched with magnetic antibody beads and analyzed by MALDI-TOF-MS
Fig. 2
Fig. 2
MALDI-TOF-Mass Spectra of SARS-CoV-2-Positive Patient Samples. (A) Tryptic peptides from SARS-CoV-2 nucleoprotein GQGVPINTNSSPDDQIGYYR (peptide A), GQGVPINTNSSPDDQIGYYRR (peptide Aext) and AYNVTQAFGR (peptide C) as well as the isotope-labeled peptides SIL-A and SIL-C (Table 1) are highlighted. (B) Diagnostic peptides from SARS-CoV-2 nucleoprotein (peptides C and SIL-C) are shown enlarged
Fig. 3
Fig. 3
Overview of 53 SARS-CoV-2-Positive Nasopharyngeal Samples. Ct values in RT-qPCR are compared to the concentration of peptide C from SARS-CoV-2 nucleoprotein as determined by MALDI-TOF-MS in the same samples
Fig. 4
Fig. 4
Discrimination of SARS-CoV-2 “Delta Variant” from other Viral Strains. (A) MRM chromatogram of a SARS-CoV-2-positive patient sample with selected transitions for peptide B (NPANNAAIVLQLPQGTTLPK), peptide C (AYNVTQAFGR, and peptide D (ADETQALPQR). (B) MRM chromatogram of a SARS-CoV-2-positive sample with selected transitions for peptides B and C. (C) MALDI-TOF mass spectra of SARS-CoV-2 strain B.1.1.529 “omicron variant” (black) and SARS-CoV-2 strain B.1.617.2 “delta variant” (blue) from nasopharyngeal samples. Peptide D (ADETQALPQR), peptide Dext(KADETQALPQR), peptide D(D377Y) (AYETQALPQR), and peptide D(D377Y)ext(KAYETQALPQR) are highlighted. Peptides A (GQGVPINTNSSPDDQIGYYR), Aext(GQGVPINTNSSPDDQIGYYRR), and isotope-labeled peptide SIL-A (GQGVPINTNSSPDDQIGYYR*) are visible in both samples
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