We have been working for some time on two related ideas in transcriptomics and proteomics, the use of transcriptomes to infer proteomes and combining quantitative transcriptomics and proteomics to gain deeper understanding of how viral infections affect the host cell. These ideas were first put forward 2 years ago in the technique we named PIT analysis - Proteomics Informed by Transcriptomics. In this talk I will quickly outline how the concept works before providing some short examples of how we have used it to analyse viral infections from a deeper analysis of how a common cold virus (adenovirus) affects host cell ubiquitination to how a zoonotic virus (Hendra virus) distinctly affects bat cells and human cells during infection. Critically we will show how direct RNA sequencing (third generation transcriptomics) can be used to proteomically uncover unexpected deletions in the protein repertoire of SARS-CoV-2 with significant impact on our understanding of SARS-CoV-2 pathogenesis and how to conduct SARS-CoV-2 vaccine trials in animals.