I would argue that mass spectrometry based proteomics is capable of offering much better insight into functional relevance than transcriptomics. Proteins carry out function... and mRNA levels are only loosely coupled to protein levels (at best, expect an R^2 < 0.4). Why measure RNA when what you really care about are proteins? People just do transcriptomics because it's cheap.

This particular paper has flaws - as you mentioned, only a very small number of peptides are measured. I work on proteomics, and I remember this discussion from when the paper was initially published: https://mstdn.social/@pwilmart@scicomm.xyz/11087205681645628...

Paleoproteomics isn't what I would call well developed at this stage. How do we know that the peptides that were detected were actually from Vlad? Many people may have handled the letters over the years.