Dataset Information

Robust high throughput proteomics identification and deami-dation quantitation of extinct species up to Pleistocene with Ultrahigh Resolution MALDI-FTICR Mass Spectrometry

ABSTRACT: Peptide mass fingerprinting (PMF) using MALDI-TOF mass spectrometry allows the identification of bone species based on their type I collagen sequence. In archaeological or paleontological field, PMF is known as ZooMS and is widely implement-ed to find markers for most species, including the extinct ones. In addition to the identification of bone species, ZooMS enables dating estimation by measuring the deamidation value of specific peptides. Herein, we report several enhancements to the classical ZooMS technique, which reduces to ten-fold the required bone sample amount (down to milligram scale) and achieves robust deamidation value calculation in a high throughput manner. These improvements rely on a 96-well plates samples preparation, a careful optimization of collagen extraction and digestion to avoid spurious posttranslational modifi-cations production and peptide mass fingerprinting at high resolution using MALDI-FTICR (Matrix Assisted Desorption Ionization Fourier Transform Ion Cyclotron Resonance) analysis. This method was applied to the identification of a hun-dred bones of herbivores from the Middle Paleolithic site of Caours (Somme, Northern France) well dated from the Eemian Last Interglacial climatic optimum. The method gave reliable species identification to bones already identified by their oste-omorphology, as well as to more challenging bone samples consisting of small or burnt bone fragments. The obtained de-amidation values of bones originating from the same geological layers have a low standard deviation. The method can be applied to archaeological bone remains and offers a robust capacity to identify traditionally unidentifiable bone fragments, thus increasing the number of identified specimens and providing invaluable information in specific contexts.

INSTRUMENT(S): Bruker Daltonics solarix series, Q Exactive Plus

ORGANISM(S): Equus Caballus (horse) Homo Sapiens (human) Bos Taurus (bovine) Castor Fiber (eurasian Beaver) Rhinoceros Cervus

TISSUE(S): Bone

SUBMITTER: BRAY FABRICE

LAB HEAD: Bray Fabrice

PROVIDER: PXD038283 | Pride | 2023-04-28

REPOSITORIES: Pride

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Project description:Paleoproteomics and the study of ancient proteins has become an important consideration in bioarchaeological research as we seek to understand the relationship between the physical skeleton and its underlying biochemistry. Osteocalcin (OC) is an abundant, non-collagenous protein that is accessible archaeologically due to its affinity for hydroxyapatite in bone. Manufactured by the osteoblast cells during normal bone metabolism, osteocalcin is inherently linked to the process of bone remodelling. Clinical studies have consistently shown the impact of biological (i.e., sex and age) and pathological (i.e., disease) factors on osteocalcin concentrations within the body; however, this connection has yet to be fully explored bioarchaeologically. For this study, 46 individuals from the Danish Sct. Albert’s cemetery (AD 1250-1536) were analyzed with cortical bone samples harvested from the femur. Each sample was demineralized and quantified using established paleoproteomic methods (ELISA) and tested for diagenesis using FTIR-ATR. 4 samples were validated by LC-MS. No significant differences were found in the osteocalcin concentrations between adult males and females. However, males had a wider range of osteocalcin variability perhaps explained in part by their increased prevalence of pathological conditions characterized by bone remodelling. Similarly, non-adults had a wide range of osteocalcin variability but there were no significant differences when compared to the adult mean. No correlations were found between osteocalcin concentrations and diagenesis suggesting that the protein can survive across a range of temporal periods and variable burial environments. While no clear pattern emerged between osteocalcin concentrations and biological and/or pathological factors, this study is significant in that it further explores the use of paleoproteomics in bioarchaeological contexts and how we may unite our macroscopic and biochemical assessments of human skeletal remains.

Dataset Information

Robust high throughput proteomics identification and deami-dation quantitation of extinct species up to Pleistocene with Ultrahigh Resolution MALDI-FTICR Mass Spectrometry

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