Proteomics
is continually being applied to a wider range of applications,
now including the analysis of archaeological samples and anatomical
specimens, particularly collagen-containing tissues such as bones
and teeth. Here, we present the application of a chemical digestion-based
proteomics sample preparation protocol to the analysis of fresh, anatomical,
and archaeological samples. We describe and discuss two protocols:
one that uses hydroxylamine as an additional step of the proteomic
workflow, applied to the insoluble fraction, and another that applies
hydroxylamine directly on demineralized bones and teeth. We demonstrate
the additional information that can be extracted using both protocols,
including an increase in the sequence coverage and number of peptides
detected in modern and archaeological samples and an increase in the
number of proteins identified in archaeological samples. By targeting
research related to collagens or extracellular matrix proteins, the
use of this protocol will open new insights, considering both fresh
and ancient mineralized samples.