Paleoproteomics

Abstract

Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human−animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.

Paleoproteomic evidence reveals dairying supported prehistoric occupation of the highland Tibetan Plateau

“…While various limitations prevent us from drawing detailed conclusions from the species data, direct evidence for the ancient milking of goat, sheep, and possibly Bovinae species was also obtained. Given that goat BLG can be more challenging to detect by liquid chromatography–tandem mass spectrometry (LC-MS/MS) ( 44 ), the dominance of goat-specific peptides in our samples would potentially suggest a preference for goat milk on the early western plateau. One animal for which no direct dairying evidence could be confirmed, surprisingly, was the yak.…”

The “ForensOMICS” approach to forensic post-mortem interval estimation: combining metabolomics, lipidomics and proteomics for the analysis of human bone

“…However, on closer inspection, the proteomic profile appears to show quite a considerable overlap between the individuals from three post-decomposition groups (i.e., 219, 790 and 834 days) suggesting that this does not provide sufficient sensitivity to be able to segregate close PMIs. This could be due to the nature of these biomolecules; proteins, in fact, have been seen to be highly stable and could be employed for long-term PMI estimation in forensic scenarios 12,13 and even in archaeological investigation of skeletal remains 43,44 . Therefore, it possible that the close and rather short PMIs included in the present study could be not fully differentiated using proteomics.…”

PaleoProPhyler: a reproducible pipeline for phylogenetic inference using ancient proteins

“…Recent advances in protein extraction and mass spectrometry [7, 8, 9] have made it possible to isolate ancient peptides from organisms that lived thousands or even millions of years ago. Certain ancient proteins have a lower degradation rate and can be preserved for longer than ancient DNA [10, 11, 12, 13]. The sequences of these proteins contain evolutionary information and thus have the potential to resolve important scientific questions about the deep past, which are not approachable via other methods.…”