Homo naledi proteins 2

As background to this work, the recovery of ancient proteins from hominid dental enamel has
previously been achieved starting from specimens up to ~2 million years old retrieved in temperate
and sub-tropical environments 1,2. The dental enamel proteome includes amelogenin, a protein that, in
humans, is expressed in two isoforms encoded in the non-recombinant regions of the
heterochromosomes, namely amelogenin X (AMELX) on the X chromosome and amelogenin Y
(AMELY) on the Y chromosome. The detection of AMELY-specific peptides allows the
straightforward assignment of the analysed dental specimen to a male individual. On the other hand,
the exclusive detection of AMELX-specific peptides is ambiguous, because it can either be
interpreted as deriving (i) from a female individual, or alternatively from (ii) a male individual whose
signal for the AMELY-specific peptides is too low to be detected, due to diagenetic degradation.
These two cases can now be discriminated with a semi-quantitative mass spectrometric approach
based on the determination of the threshold intensity of AMELX-specific peptides below which the
signal for AMELY-specific peptides is lost. This method however requires the identification of
AMELY-specific peptides in at least one dental specimen.