Paleoproteomics in 2014 vs. 2024:

Introduction

Paleoproteomics, a branch of proteomics, is the study of ancient proteins to gain insights into evolutionary biology, ancient diseases, and past environments. Paleoproteomics has transformed our understanding of the past, offering insights into evolution, ancient diseases, and diets. Over the past decade, technological and methodological advancements have deepened our knowledge of human-animal interactions, ancient environments, and the vertebrate fossil record (table 1). This essay compares current proteomics methods with those from a decade ago, emphasizing significant changes and their impact on the field.

Why Paleoproteomics?

Proteins are durable biomolecules that can survive for millions of years, often outlasting DNA. Composed of amino acid sequences with complex structures, proteins are essential for taxonomic identification and phylogenetic analysis. They also undergo post-translational modifications, increasing their biochemical complexity. While most proteins have a short lifespan, some can persist from minutes to the entire life of an organism, and secreted proteins like keratins can last for centuries. Despite carrying less genetic information than DNA, proteins provide rich, tissue-specific data that paleoproteomics leverages to explore ancient biological and cultural histories[1].

Table 1 Comparison of Instruments and Approaches Used in Ancient Protein Studies [1]

Technological Advancements

In the early 2010s, paleoproteomics experienced significant technological innovations that advanced the study of ancient proteins. One of the key developments was the application of soft ionization mass spectrometry, which made the study of ancient proteins feasible by allowing for the analysis of proteinaceous material extracted from fossils, bones, dental calculus, and other archaeological samples[1]. This technology enabled the identification of proteins and provided insights into the phylogenetic relationships of both extant and extinct species, as well as the reconstruction of ancient diets and diseases[2].

Earlier in the decade, researchers relied on mass spectrometers with lower resolution and sensitivity, such as the MALDI-TOF (Matrix-Assisted Laser Desorption/Ionization Time-of-Flight) systems. While useful, these systems had limitations in resolving complex peptide mixtures from ancient samples.

By 2024, advancements in high-resolution tandem mass spectrometry (HR-MS/MS) and data acquisition methods like DIA have significantly improved protein identification in paleoproteomics. Modern MS/MS analyses now use LC−MS/MS systems with UHPLC, nano-ESI, and Orbitrap mass spectrometers, enhancing speed, resolution, and accuracy[1].

The use of isotope ratio mass spectrometry (IRMS) in archaeology has expanded as techniques have become more efficient and cost-effective. Over time, isotopic analysis has broadened, addressing paleoclimate, paleoenvironmental reconstruction, mobility, origin, and life history[3]. The exploration of novel isotope systems, such as zinc isotopes in Neanderthals, provides new insights, especially when collagen preservation is poor, as seen in studies linking isotopic evidence to dietary habits[4].