Proteomic and metabolomic analysis of COVID-19 nasal swabs

The epithelial barrier's primary role is to protect against entry of foreign and pathogenic elements. Global and targeted approaches were applied to nasal swabs from healthy and COVID-19-confirmed cases within 24 hours post-positive-confirmation and at 3 weeks post-infection to observe changes in proteome and metabolome.
We found that the tryptophan/kynurenine metabolism pathway is a pinch-point regulator of canonical and non-canonical transcription activation, macrophage release of cytokines and significant changes in the immune and metabolic status with increasing severity and disease course., Nasal epithelial swabs were self-collected by participants in this study. Swabs were resuspended in 80% methanol with 6mg of 1.0 mm zirconium beads and used cell shearing to extract proteins and metabolites. The method is described in Wasinger et al., 2020 [1]. Proteins were pelleted and the supernatant containing metabolites stored at -80°C until required. Protein pellet was resuspended in digestion buffer and 50 µg enzymatically treated with trypsin overnight at room temperature.
Proteomic mass spectrometry
Mass spectrometry was carried out using a QExactive (Thermo Electron, Bremen, Germany)  run in DDA mode using 1.5 μg (2.0 μL from 10μL) as previously described [2]. Peptides were eluted using a linear gradient of H2O:CH3CN (98:2, 0.1% formic acid) to H2O:CH3CN (64:36, 0.1% formic acid) at 250 nL min-1 over 60 min.
Statistical Analysis
Proteins were identified using Mascot Daemon v2.5.1 (Matrix Science, London, UK) searched against the SwissProt and SARV19 database (downloaded Febr..., Microsoft Word
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