Extended Data Fig. 2: Proteome-sequence coverage for specimen Dm.5/157-16635.
From: Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny
a, c, e, g, i, j, Peptide–spectrum match (PSM) sequence coverage of the proteins AMBN (a), ENAM (c), AMELX (e), AMTN (g), MMP20 (i) and ALB (j). Annotations include ‘amino acid position, amino acid called in that position (number of PSMs and peptides covering that position)’ for the phylogenetically informative single-amino-acid polymorphisms within Rhinocerotidae. b, d, f, h, Frequency (per cent) of phosphorylated (green) and unphosphorylated (red) PSMs per amino acid position for AMBN (b), ENAM (d), AMELX (f) and AMTN (h). Numbers within the bars provide the PSM counts. k, Violin plot of distribution of PSM coverage for all covered sites (n = 693), and for sites of phylogenetic relevance (single-amino-acid polymorphisms, n = 30). The box plots define the range of the data, with whiskers extending to 1.5× interquartile range, boxes denoting the 25th and 75th percentiles and dots indicating the median. All panels are based only on MaxQuant search results. The Supplementary Data contains examples of MS/MS spectra, and fragment-ion series alignments for each of the marked single-amino-acid polymorphisms.
