Palaeoproteomics
14 workflows · 2016–2026
Palaeoproteomics: Ancient enamel, bone and eggshell, where the proteins are damaged and the species may be extinct. 14 catalogued workflows and 14 papers.
Ancient enamel, bone and eggshell, where the proteins are damaged and the species may be extinct.
| Workflows | 14 |
| Papers | 14 |
| Authors | 195 |
| Active | 2016-09-27 to 2026-09-09 |
Workflows (14)
- Ancient ostrich eggshell proteome (2016): Sequencing of ancient peptides bound to ostrich eggshell mineral surfaces, demonstrating protein survival into deep time (~3.8 million years) via de novo MS/MS workflows.
- Palaeoshellomics of prehistoric mother-of-pearl ornaments (2019): First palaeoproteomics of mollusc shell. De novo sequences from archaeological ornaments and reference shells were compared database-independently, showing Neolithic double-buttons were made from freshwater mother-of-pearl.
- Stephanorhinus enamel proteome (2019): Palaeoproteomic enamel-protein workflow on a 1.77-million-year-old Stephanorhinus tooth from Dmanisi, resolving rhinoceros phylogeny beyond the reach of ancient DNA.
- Gigantopithecus enamel proteome (2019): Palaeoproteomic de novo workflow that recovered the enamel proteome of a 1.9-million-year-old Gigantopithecus blacki molar from Chuifeng Cave, placing it as an early-diverging pongine.
- Homo antecessor enamel proteome (2020): Palaeoproteomic de novo + tag-search workflow that recovers enamel proteome from a ~800,000-year-old Homo antecessor tooth and uses the resulting sequences to place the lineage on the hominin tree.
- Leopard Cave antelope collagen palaeoproteomics (2020): Palaeoproteomic species identification of Later Stone Age remains from Leopard Cave, Namibia, using de novo derived type I collagen sequences proposed for wild antelopes. The remains thought to be early domestic caprines turned out to be a wild antelope.
- South American camelid hair fibre peptides (2021): Distinguishes guanaco, vicuna, llama and alpaca fibres, including archaeological samples, with taxonomic keratin peptides found by database-assisted de novo sequencing and molecular networking.
- Woolly mammoth trunk collagen and metaproteome (2022): Metaproteomic analysis of two 30,000-year-old mammoth trunks with PEAKS de novo and SPIDER homology search, characterising collagen I alpha-1 and alpha-2 sequences and three candidate diagnostic amino acid substitutions.
- Paranthropus robustus enamel proteome (2025): Palaeoproteomic sequencing of enamel peptides from four Paranthropus robustus teeth at Swartkrans, assigning sex from AMELY peptides and detecting a polymorphism that hints at subgroups.
- Harbin cranium proteome (2025): Palaeoproteomic sequencing of 95 endogenous proteins from the Harbin (Homo longi) cranium, whose Denisovan-derived amino acid variants place the individual in a Denisovan population.
- Archaeological amphora residue proteomics (thesis) (2026): Thesis optimising bottom-up proteomics with de novo sequencing for protein traces in archaeological ceramics, demonstrating tuna in first-century amphorae; other chapters cover lipidomics and nanoparticle synthesis.
- Ozboneprot (2026): Workflow for de novo sequencing and validation of bone proteins to support shotgun palaeoproteomics on Australian zooarchaeological and palaeontological samples.
- Homo erectus enamel proteome (China) (2026): Enamel proteome of six roughly 0.4-million-year-old Homo erectus specimens from Zhoukoudian, Hexian and Sunjiadong, sequenced with PEAKS, revealing a novel AMBN variant shared by all of them.
- Bianfu Cave Denisovan proteome (2026): Palaeoproteomic sequencing of bone and tooth proteins from Bianfu Cave in Southwest China, combining PEAKS de novo and homology searches, that assigns three bone fragments and two teeth to Denisovans.
Papers (14)
- Protein sequences bound to mineral surfaces persist into deep time (2016, eLife, peer-reviewed)
- ’Palaeoshellomics’ reveals the use of freshwater mother-of-pearl in prehistory (2019, eLife, peer-reviewed)
- Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny (2019, Nature, peer-reviewed)
- Enamel proteome shows that Gigantopithecus was an early diverging pongine (2019, Nature, peer-reviewed)
- The dental proteome of Homo antecessor (2020, Nature, peer-reviewed)
- Palaeoproteomics gives new insight into early southern African pastoralism (2020, Scientific Reports, peer-reviewed)
- Untangling the fibre ball: Proteomic characterization of South American camelid hair fibres by untargeted multivariate analysis and molecular networking (2021, Journal of Proteomics, peer-reviewed)
- Meta-proteomic analysis of two mammoth’s trunks by EVA technology and high-resolution mass spectrometry for an indirect picture of their habitat and the characterization of the collagen type I, alpha-1 and alpha-2 sequence (2022, Amino Acids, peer-reviewed)
- Enamel proteins reveal biological sex and genetic variability in southern African Paranthropus (2025, Science, peer-reviewed)
- The proteome of the late Middle Pleistocene Harbin individual (2025, Science, peer-reviewed)
- Methodological development in proteomics and lipidomics applied to the analysis of cultural heritage samples : photochemical synthesis of metallic nanoparticles in flow (2026, thesis)
- Ozboneprot: A de novo sequencing workflow to enable shotgun palaeoproteomics on Australian zooarchaeological and paleontological samples (2026, Research Square, preprint)
- Enamel proteins from six Homo erectus specimens across China (2026, Nature, peer-reviewed)
- Ancient proteins identify various Denisovan remains from Southwest China (2026, Nature, peer-reviewed)
Sequencing tools these papers used
Where the work happened
Australia, Canada, China, Denmark, France, Georgia, Germany, Greenland, Ireland, Israel, Italy, Kenya, Luxembourg, Malaysia, Namibia, Norway, Russia, South Africa, Spain, Sweden, Tanzania, UK, USA