As head of the ancient biomolecules laboratories at the University of Manchester, my interests revolve around the use of ancient proteins and DNA for the study of human history, particularly in their application to human impacts on biodiversity in the past through to the present. I am also currently a Royal Society University Senior Research Fellow which allows me to dedicate time to investigating the information content of the bone proteome, with a particular interest in protein decay in the extracellular matrix that spans forensic, archaeological and palaeontological applications through to better understanding modern repair mechanisms.

In 2008 I completed my NERC-funded PhD entitled ‘Species identification in ancient and degraded bone fragments using protein mass spectrometry’ in the Department of Biology, University of York which initially focussed on sequencing the small non-collagenous bone protein osteocalcin by LC-ESI-qTOF-MS and LC-MALDI-TOF-TOF-MS. I then re-directed this research to the study of bone collagen (I), because of its greater persistence in fossilised remains, and developed ZooMS (‘Zooarchaeology by Mass Spectrometry’), in which collagen peptides are fractionated by SPE and fingerprinted using MALDI-TOF-MS. Typical archaeological applications are to distinguish between morphologically-similar taxa such as the caprine species, sheep and goats, or the identification of taxa in limited but highly assemblages spanning much of the Pleistocene. During my postdoctoral research I refined this methodology to work on other collagen-based samples, ranging from mummified skin and leathers, meat and bone meal and gelatine-containing food products, as well as other mineralised tissues such as ostrich eggshell.

In 2010 I moved to the Faculty of Life Sciences here at the University of Manchester to take up a NERC-funded postdoctoral research fellowship on the assessment of biodiversity in Pleistocene Britain through comprehensive small-scale microsampling of vertebrate fossil remains. In 2013 I was awarded my Royal Society University Research Fellowship (until 2018) on 'Molecular Timers'.

Bone Biochemistry: Ancient and Degraded Proteins

Most of my research uses protein separation and analysis techniques, particularly 'soft-ionization' mass spectrometry, to investigate degradation in modern and ancient tissues ranging from processed foods to those found in archaeological and palaeontological burial environments. The 'soft-ionization' methods we typically use are Matrix Assisted Laser Desorption Ionization (MALDI) for high-throughput peptide mass fingerprinting (PMF) of samples, and Electrospray Ionization (ESI), which we dedicate for more in-depth sequence analysis. It is the 'soft-ionization' that allows for the analysis of large biomolecules without inducing excessive fragmentation prior to analysis and detection in the mass spectrometer, ideal for studying low quantities of ancient and degraded proteins. We also now make inferences from our proteomics research to guide ancient DNA analyses for greater information in a more targetted manner.

Biomolecular Species Identification in Forensics and Archaeology

Despite early research into the survival of non-collagenous bone proteins such as the small mineral-binding protein osteocalcin, most of my research focuses on the dominant bone protein type 1 collagen because of its structural properties making it highly insoluble, resulting in enhanced survival. During my PhD I developed a method of 'fingerprinting' collagen peptides using a limited fractionation method that separated highly conserved collagen peptides from the more variable ones. Once I discovered that collagen fingerprinting could distinguish between the major domesticate animals used in animal husbandry, including the morphologically similar skeletal remains of sheep and goat, we named the technique ZooMS, after 'Zooarchaeology by Mass Spectrometry'. In archaeological applications we typically use the species identifications to investigate likely animal husbanding practises in the past, where my research has mainly focused on early Near Eastern agriculture including work in Cyprus and south-east Turkey on samples >10,000 years old.

Palaeobiodiversity and Vertebrate Evolution

My current research uses high-throughput ZooMS to investigate how vertebrate biodiversity has changed in Britain over the past few million years, focusing on ~20,000 bone fragments excavated from deposits at the back of Pin Hole Cave, Derbyshire (in collaboration with Creswell Crags Heritage Centre and Manchester Museum) dating back approximately 50,000 years. I am also interested in the phylogenetic inferences we can make using protein sequencing, which have included working on ~650,000 year old mammoth remains from Britain, ~3.5 million year old giant camel fossils discovered in the High Arctic, as well as other more enigmatic species such as the dodo.

My research focuses in two main areas: 1) the use of cutting-edge omics methods to investigate ageing in extracellular tissues, whether the biological ageing process in modern tissues, or the geological ageing process in ancient tissues, and 2) the development and application of biomolecular methods in the study of human impacts on biodiversity, both in the past and present.

Overlapping with both of these areas is the use of palaeoproteomics - the study of ancient proteins through proteomic methods - proteins can tell us both about the changing structure of tissues, as well as be informative of species. Despite early research into the survival of non-collagenous bone proteins such as the small mineral-binding protein osteocalcin, most of my research focuses on type 1 collagen which is the major protein in bone and one of the most abundant in the animal kingdom. ZooMS, after 'Zooarchaeology by Mass Spectrometry', is what we call our approach to using protein fingerprints to differentiate between different taxa, which is particularly useful for fragmentary archaeological bone or the remains of juvenile individuals from morphologically similar species, such as sheep and goat. In archaeological applications we typically use the species identifications to investigate likely animal husbanding practises in the past, where my research has mainly focused on early Near Eastern agriculture including work in Cyprus and south-east Turkey. My current research uses molecular methods, such as high-throughput ZooMS, to investigate how vertebrate biodiversity has changed during the evolution of humans, but I am also investigating how collagen sequencing can aid our understanding of phylogenetic relationships among long extinct taxa from palaeontological sites worldwide.

Self-funded PhD projects in 'Ancient Proteins'

Archaeological animal remains offer insights into how our ancestors interacted with our natural environment, as well as how we came to domesticate a range of species that we now rely on as a source of food and other resources. However, skeletal remains in the archaeological record are often fragmentary, leaving large proportions of this valuable resource unused. This project seeks to explore the current limitations and further develop proteomics-based methods that can objectively identify fragmentary remains from archaeological sites; in the zooarchaeological community this is known as ZooMS. We welcome project suggestions for a wide range of animal vertebrate groups, ranging from mammals to fish, and from any geographical area of interest.

The student would have the opportunity to gain experience with the morphological analysis and digital recording of archaeological skeletal remains, and will be trained in the use of various proteomics-based techniques, including Matrix Assisted Laser Desorption Ionization (MALDI) and Electrospray Ionization (ESI) mass spectrometry.

Contact [email protected] for further enquiries and the potential for funding.

Samantha Hook (PhD student)

I am a NERC DTP-CASE student at The University of Manchester, focussing on quantifying the genetic health of sharks and rays (elasmobranchs), in both captive and wild environments.

Virginia Harvey (PhD student)

My Dean’s award scholarship allows me to research the impact of humans on marine vertebrates (primarily turtles and fish) in archaeological deposits.

Elisabeth Johnston (PhD student)

My scholarship is funded by the Royal Society and I work on forensic proteomics, with a particular interest in the development of improved omic techniques for age estimation.

Manasij Pal Chowdhury (PhD student)

With my President's award scholarship I study multiomic approaches to the analysis of archaeological food residues.

Dr Karren Palmer (PDRA)

I am a PDRA funded as part of the ERC-funded ASIAPAST project which carries out biomolecular and zooarchaeological investigations of mobile pastoralism in the ancient Eurasian steppe.

Andy Baker (PhD student)

Through my BBSRC-DTP award I investigate a range of bioinformatic approaches to the analysis of marine animals, with a particular interest in machine learning.

Past Members:

Dr Noemi Procopio (former PhD student)

Dr Caroline Wadsworth (former PhD student)

Dr Soyab Patel (former PDRA)