Identification of Endogenous Peptides in Nasal Swab Transport Media used in MALDI-TOF-MS Based COVID-19 Screening

Mass spectrometry
(MS) based diagnostic detection of 2019 novel
coronavirus infectious disease (COVID-19) has been postulated to be
a useful alternative to classical PCR based diagnostics. These MS
based approaches have the potential to be both rapid and sensitive
and can be done on-site without requiring a dedicated laboratory or
depending on constrained supply chains (i.e., reagents and consumables).
Matrix-assisted laser desorption ionization (MALDI)–time-of-flight
(TOF) MS has a long and established history of microorganism detection
and systemic disease assessment. Previously, we have shown that automated
machine learning (ML) enhanced MALDI-TOF-MS screening of nasal swabs
can be both sensitive and specific for COVID-19 detection. The underlying
molecules responsible for this detection are generally unknown nor
are they required for this automated ML platform to detect COVID-19.
However, the identification of these molecules is important for understanding
both the mechanism of detection and potentially the biology of the
underlying infection. Here, we used nanoscale liquid chromatography
tandem MS to identify endogenous peptides found in nasal swab saline
transport media to identify peptides in the same the mass over charge
(m/z) values observed by the MALDI-TOF-MS
method. With our peptidomics workflow, we demonstrate that we can
identify endogenous peptides and endogenous protease cut sites. Further,
we show that SARS-CoV-2 viral peptides were not readily detected and
are highly unlikely to be responsible for the accuracy of MALDI based
SARS-CoV-2 diagnostics. Further analysis with more samples will be
needed to validate our findings, but the methodology proves to be
promising.