Extended Data Fig. 4: Comparison of HCl and TFA extraction protocols.
From: Enamel proteome shows that Gigantopithecus was an early diverging pongine
a, Summed and normalized peptide intensities for each combination of peptide length and number of acidic residues (aspartic acid, glutamic acid, deamidated asparagine, deamidated glutamine). Circle sizes are proportional to the percentage of the total intensity, for each combination of peptide length and number of acidic residues. b, Summed and normalized intensities by peptide length. c, Summed and normalized peptide intensities across peptide hydrophobicity (GRAVY index values calculated using the R package Peptides, scale ‘KyteDoolittle’). Insets show peptide count distribution across peptide hydrophobicity. d, Extraction performance for various data categories. Values scaled to one and compared to the best-performing extraction method for each category independently. SAPs refer to those SAPs informative within Hominoidea. e, Proportional Venn diagram of unique peptide sequences identified in the two demineralization methods. All comparisons based on MaxQuant LFQ data only. N, number of peptides.
