Figure 2.

Demonstration of taxonomic uncertainties from a ZooMS/MS output file. (A). Unipept³⁶ sunburst view on Mascot result of Homo sapiens reference sample of Rüther et al.⁸ showing uniqueness of peptide stretches on different taxonomic levels (Figure S1). Sunburst plot is colored via phylogenetic relatedness. (B). Histogram showing the percentage amino acid distribution between the human reference proteome (UP000005640), collected from Uniprot (red) and solely collagen sequences extracted from the same human proteome from Uniprot (blue). (C). Demonstrative overview of Homo sapiens collagen peptides, alongside the top results with similar Mascot scoring. Due to an isobaric switch the protein of origin and species of origin can change. Unfortunately, intensity prediction and the accompanying MS²PIP⁶³ score does not always change either, compromising this second-pass solution to further filter the peptide results.