The capabilities of bioanalytical mass spectrometry to (i) detect and differentiate viruses at the peptide level whilst maintaining high sample throughput and (ii) to provide diagnosis and prognosis for infected patients are presented as a tutorial in this work to aid analytical chemists and physicians to gain insights into the possibilities offered by current high-resolution mass spectrometry technology and bioinformatics. From (i) sampling to sample treatment; (ii) Matrix-Assisted Laser Desorption Ionization- to Electrospray Ionization -based mass spectrometry; and (iii) from clustering to peptide sequencing; a detailed step-by-step guide is provided and exemplified using SARS-CoV-2 Spike Y839 variant and the variant of concern SARS-CoV-2 Alpha (B.1.1.7 lineage), Influenza B, and Influenza A subtypes AH1N1pdm09 and AH3N2.Highlights: - Immunohistochemistry with magnetic core nanoparticles to isolate viruses. - The use of MALDI-MS for rapid virus detection is explained in detail; - The use of ESI-MS/MS to pinpoint host-patient crosstalk is explained in detail. - The absolute quantitative MS is explained for large-scale protein quantitation.This work received financial support from PT national funds (FCT/MCTES) through the projects UIDB/50006/2020 and UIDP/50006/2020 and from PROTEOMASS Scientific Society through the projects #PM001/2019 and #PM003/2016.info:eu-repo/semantics/publishedVersio
