References

Amino acids in fossils

1954 · External reference

The emerging landscape of single-molecule protein sequencing technologies

10.1038/s41592-021-01143-1 · 2021 · External reference

Unraveling the human bone microenvironment beyond the classical extracellular matrix proteins: a human bone protein library

10.1021/pr200522n · 2011 · External reference

When data sharing gets close to 100%: what human paleogenetics can teach the open science movement

10.1371/journal.pone.0121409 · 2015 · External reference

Early Holocene preservation differences between cortical and trabecular bone proteomes

10.1016/j.jasrep.2024.104643 · 2024 · External reference

Untangling the fibre ball: Proteomic characterization of South American camelid hair fibres by untargeted multivariate analysis and molecular networking

10.1016/j.jprot.2020.104040 · 2021 · External reference

A novel LC system embeds analytes in pre-formed gradients for rapid, ultra-robust proteomics

10.1074/mcp.tir118.000853 · 2018 · External reference

Machine Learning for collagen peptide biomarker determination in the taxonomic identification of archaeological fish remains

10.1016/j.jasrep.2023.104001 · 2023 · External reference

Non-invasive Paleo-metabolomics and Paleo-proteomics analyses reveal the complex funerary treatment of the early 18th Dynasty dignitary NEBIRI (QV30)

10.3390/molecules27217208 · 2022 · External reference

An Optimized Approach for Protein Residue Extraction and Identification from Ceramics After Cooking

10.1007/s10816-011-9120-5 · 2012 · External reference

Mixed results of seven methods for organic residue analysis applied to one vessel with the residue of a known foodstuff

10.1016/j.jas.2006.03.010 · 2007 · External reference

Proteomic and N-Terminomic TAILS Analyses of Human Alveolar Bone Proteins: Improved Protein Extraction Methodology and LysargiNase Digestion Strategies Increase Proteome Coverage and Missing Protein Identification

10.1021/acs.jproteome.9b00445 · 2019 · External reference

Ancient DNA data hold insights into past organisms and ecosystems - handle them with more care

10.1038/d41586-024-03993-z · 2024 · External reference

Byonic: advanced peptide and protein identification software

10.1002/0471250953.bi1320s40 · 2012 · External reference

Next Generation Lab puts Denmark's past in the hands of its future

10.15184/aqy.2021.170 · 2022 · External reference

Species identification of archaeological skin objects from Danish bogs: comparison between mass spectrometry-based peptide sequencing and microscopy-based methods

10.1371/journal.pone.0106875 · 2014 · External reference

Illuminating 'the ugly side of science': fresh incentives for reporting negative results

10.1038/d41586-024-01389-7 · 2024 · External reference

Identifying ZooMS Spectra (mammals) using mMass

2021 · External reference

On the standardization of ZooMS nomenclature

10.1016/j.jprot.2020.104041 · 2021 · External reference

Zooarchaeology by Mass Spectrometry (ZooMS) for bone material - AmBiC protocol

10.17504/protocols.io.bffdjji6 · 2020 · External reference

Examining collagen preservation through glutamine deamidation at Denisova Cave

10.1016/j.jas.2021.105454 · 2021 · External reference

An ancient residue metabolomics-based method to distinguish use of closely related plant species in ancient pipes

10.3389/fmolb.2020.00133 · 2020 · External reference

Ancient collagen reveals evolutionary history of the endemic South American 'ungulates'

10.1098/rspb.2014.2671 · 2015 · External reference

Species identification by analysis of bone collagen using matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry

10.1002/rcm.4316 · 2009 · External reference

Species identification of archaeological marine mammals using collagen fingerprinting

10.1016/j.jas.2013.08.021 · 2014 · External reference

Stop hoarding ancient bones, plead archaeologists

10.1038/nature.2017.22445 · 2017 · External reference

Proteomic analysis of a pleistocene mammoth femur reveals more than one hundred ancient bone proteins

10.1021/pr200721u · 2012 · External reference

Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny

10.1038/s41586-019-1555-y · 2019 · External reference

The CARE principles for indigenous data governance

10.5334/dsj-2020-043 · 2020 · External reference

The PLOS ONE collection on machine learning in health and biomedicine: Towards open code and open data

10.1371/journal.pone.0210232 · 2019 · External reference

The past, present and future of Registered Reports

10.1038/s41562-021-01193-7 · 2022 · External reference

A late Middle Pleistocene Denisovan mandible from the Tibetan Plateau

10.1038/s41586-019-1139-x · 2019 · External reference

Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine

10.1038/nbt.4236 · 2018 · External reference

Orthrus: an AI-powered, cloud-ready, and open-source hybrid approach for metaproteomics

10.1101/2024.11.15.623814 · 2024 · External reference

lesSDRF is more: maximizing the value of proteomics data through streamlined metadata annotation

10.1038/s41467-023-42543-5 · 2023 · External reference

Peptide sequences from the first Castoroides ohioensis skull and the utility of old museum collections for palaeoproteomics

10.1098/rspb.2016.0593 · 2016 · External reference

Biologically and diagenetically derived peptide modifications in moa collagens

10.1098/rspb.2015.0015 · 2015 · External reference

An application of zooms to identify archaeological avian fauna from Teotihuacan, Mexico

10.1016/j.jas.2022.105692 · 2022 · External reference

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

10.1038/nbt.1511 · 2008 · External reference

A proteomics sample metadata representation for multiomics integration and big data analysis

10.1038/s41467-021-26111-3 · 2021 · External reference

Recommendation of: Open science, communication, and collaboration for the future of palaeoproteomics. Round#2

10.24072/pci.archaeo.100601 · 2025 · External reference

An unclean slate, discrepancies between food input and recovered protein signal from experimental foodcrusts

10.1101/2025.02.03.636240 · 2025 · External reference

Open science, communication, and collaboration for the future of palaeoproteomics

10.5281/zenodo.15690650 · 2025 · External reference

Ancient proteins resolve controversy over the identity of Genyornis eggshell

10.1073/pnas.2109326119 · 2022 · External reference

A Middle Pleistocene Denisovan molar from the Annamite Chain of northern Laos

10.1038/s41467-022-29923-z · 2022 · External reference

The ProteomeXchange consortium at 10 years: 2023 update

10.1093/nar/gkac1040 · 2023 · External reference

Proteomic identification of beer brewing products in the ground layer of Danish Golden Age paintings

10.1126/sciadv.ade7686 · 2023 · External reference

Amino acid dating of Pleistocene mammalian enamel from the River Thames terrace sequence: a multi-taxon approach

10.1016/j.quageo.2024.101543 · 2024 · External reference

Peptide mass fingerprinting of preserved collagen in archaeological fish bones for the identification of flatfish in European waters

10.1098/rsos.220149 · 2022 · External reference

Identifying archaeological leather – discussing the potential of grain pattern analysis and zooarchaeology by mass spectrometry (ZooMS) through a case study involving medieval shoe parts from Denmark

10.1016/j.culher.2019.04.008 · 2019 · External reference

Proteomic analysis of human tooth pulp: proteomics of human tooth

10.1016/j.joen.2014.07.001 · 2014 · External reference

Classification of collagens via peptide ambiguation, in a paleoproteomic LC-MS/MS-based taxonomic pipeline

10.1021/acs.jproteome.4c00962 · 2025 · External reference

The impact of cooking and burial on proteins: a characterisation of experimental foodcrusts and ceramics

10.1098/rsos.240610 · 2024 · External reference

A comparison of minimally-invasive sampling techniques for ZooMS analysis of bone artifacts

10.1016/j.jasrep.2022.103738 · 2023 · External reference

A unified protocol for simultaneous extraction of DNA and proteins from archaeological dental calculus

10.1016/j.jas.2020.105135 · 2020 · External reference

Digging deeper into ancient skeletal proteomes through consecutive digestion with multiple proteases

10.1016/j.jprot.2024.105143 · 2024 · External reference

Cleaning the dead: Optimized decontamination enhances palaeoproteomic analyses of a Pleistocene hominin tooth from Khudji, Tajikistan

10.1016/j.jas.2025.106228 · 2025 · External reference

The evolution and changing ecology of the African hominid oral microbiome

10.1073/pnas.2021655118 · 2021 · External reference

Animal origin of 13th-century uterine vellum revealed using noninvasive peptide fingerprinting

10.1073/pnas.1512264112 · 2015 · External reference

So you want to do biocodicology? A field guide to the biological analysis of parchment

10.1186/s40494-019-0278-6 · 2019 · External reference

Ethical guidance in human paleogenomics: New and ongoing perspectives

10.1146/annurev-genom-120621-090239 · 2022 · External reference

Protein sequencing, one molecule at a time

10.1146/annurev-biophys-102121-103615 · 2022 · External reference

The survival of β-lactoglobulin peptides in the archaeological record: Vulnerability vs. Sequence variation

10.1101/2024.09.13.612646 · 2024 · External reference

Multi-omic detection of Mycobacterium leprae in archaeological human dental calculus

10.1098/rstb.2019.0584 · 2020 · External reference

A guideline for reporting experimental protocols in life sciences

10.7717/peerj.4795 · 2018 · External reference

Semi-supervised machine learning for automated species identification by collagen peptide mass fingerprinting

10.1186/s12859-018-2221-3 · 2018 · External reference

Palaeoproteomic identification of the original binder and modern contaminants in distemper paints from Uvdal stave church, Norway

10.1038/s41598-024-63455-4 · 2024 · External reference

A comparative study of commercially available, minimally invasive, sampling methods on Early Neolithic humeri analysed via palaeoproteomics

10.1016/j.jas.2024.106002 · 2024 · External reference

Species identification of ancient Lithuanian fish remains using collagen fingerprinting

10.1016/j.jas.2018.07.006 · 2018 · External reference

Phylogenetic analyses of ray-finned fishes (Actinopterygii) using collagen type I protein sequences

10.1098/rsos.201955 · 2021 · External reference

Comment on the letter of the Society of Vertebrate Paleontology (SVP) dated April 21, 2020 regarding “Fossils from conflict zones and reproducibility of fossil-based scientific data”: the importance of private collections

10.1007/s12542-020-00522-x · 2020 · External reference

Ancient protein analysis in archaeology

10.1126/sciadv.abb9314 · 2021 · External reference

Proteomic evidence of dietary sources in ancient dental calculus

2018 · External reference

A guide to ancient protein studies

10.1038/s41559-018-0510-x · 2018 · External reference

How to get your goat: automated identification of species from MALDI-ToF spectra

10.1093/bioinformatics/btaa181 · 2020 · External reference

Species identification of Oetzi's clothing with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry based on peptide pattern similarities of hair digests

10.1002/rcm.3679 · 2008 · External reference

Concluding Commentary

10.7551/mitpress/15190.001.0001 · 2024 · External reference

Biomolecular characterization of 3500-year-old ancient Egyptian mummification balms from the Valley of the Kings

10.1038/s41598-023-39393-y · 2023 · External reference

Distinguishing African bovids using Zooarchaeology by Mass Spectrometry (ZooMS): New peptide markers and insights into Iron Age economies in Zambia

10.1371/journal.pone.0251061 · 2021 · External reference

Quantitative metaproteomics of medieval dental calculus reveals individual oral health status

10.1038/s41467-018-07148-3 · 2018 · External reference

Unresolved reference

2022 · External reference

Highly accurate protein structure prediction with AlphaFold

10.1038/s41586-021-03819-2 · 2021 · External reference

Proteomic analysis of dentin-enamel junction and adjacent protein-containing enamel matrix layer of healthy human molar teeth

10.1111/eos.12594 · 2019 · External reference

Identification of collagen-based materials in cultural heritage

10.1039/c3an00925d · 2013 · External reference

Minimally Invasive Sampling of Surface Coatings for Protein Identification by Peptide Mass Fingerprinting: A Case Study with Photographs

10.1080/01971360.2019.1656446 · 2020 · External reference

Characterization of an unusual coating on funerary portraits from Roman Egypt circa 100-300AD

10.1186/s40494-023-00908-5 · 2023 · External reference

The effect of using an inappropriate protein database for proteomic data analysis

10.1371/journal.pone.0020873 · 2011 · External reference

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics

10.1038/nmeth.4256 · 2017 · External reference

The Trouble with Ancient DNA

2025 · External reference

Petrous fever: The gap between ideal and actual practice in ancient DNA research

10.1086/733328 · 2024 · External reference

The benefits of preregistration and Registered Reports

10.1080/2833373x.2024.2376046 · 2024 · External reference

Data integration in biological research: an overview

10.1186/s40709-015-0032-5 · 2015 · External reference

Increasing sustainability in palaeoproteomics by optimizing digestion times for large-scale archaeological bone analyses

10.1016/j.isci.2024.109432 · 2024 · External reference

Evaluating the effect of database inflation in proteogenomic search on sensitive and reliable peptide identification

10.1186/s12864-016-3327-5 · 2016 · External reference

Albumin systematics of the extinct mammoth and Tasmanian wolf

10.1038/291409a0 · 1981 · External reference

Palaeoproteomic Profiling of Conservation Layers on a 14th Century Italian Wall Painting

10.1002/anie.201713020 · 2018 · External reference

Do I have something in my teeth? The trouble with genetic analyses of diet from archaeological dental calculus

10.1016/j.quaint.2020.11.019 · 2020 · External reference

Pleistocene geochronology and palaeothermometry from protein diagenesis in ostrich eggshells: implications for the evolution of modern humans

10.1098/rstb.1992.0092 · 1992 · External reference

10.24072/pcjournal.230 · 2023 · Admitted local publication

Peptide mass fingerprinting as a tool to assess micromammal biodiversity in Pleistocene South Africa: The case of Klipdrift Shelter

10.1016/j.quascirev.2023.108380 · 2023 · External reference

Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus

10.1073/pnas.2102116118 · 2021 · External reference

14th Annual Meeting of the European Society for the study of Human Evolution Abstracts Zagreb, 11-15 September 2024

2024 · External reference

The choice of search engine affects sequencing depth and HLA class I allele-specific peptide repertoires

10.1016/j.mcpro.2021.100124 · 2021 · External reference

Paleoproteomics sheds light on million-year-old fossils

10.1038/s41580-024-00803-2 · 2024 · External reference

10.24072/pcjournal.344 · 2023 · Admitted local publication

A chronological framework for the British Quaternary based on Bithynia opercula

10.1038/nature10305 · 2011 · External reference

Open-Source and FAIR Research Software for Proteomics

10.1021/acs.jproteome.4c01079 · 2025 · External reference

Probability-based protein identification by searching sequence databases using mass spectrometry data

10.1002/(sici)1522-2683(19991201)20:18<3551::aid-elps3551>3.0.co;2-2 · 1999 · External reference

Quantifying inter-laboratory variability in stable isotope analysis of ancient skeletal remains

10.1371/journal.pone.0102844 · 2014 · External reference

Species identification of Australian marsupials using collagen fingerprinting

10.1098/rsos.211229 · 2021 · External reference

Bone collagen from subtropical Australia is preserved for more than 50,000 years

10.1038/s43247-023-01114-8 · 2023 · External reference

Palaeoproteomics protocol - arid environment samples

10.17504/protocols.io.yxmvmn1kog3p/v1 · 2023 · External reference

Assessment of different screening methods for selecting palaeontological bone samples for peptide sequencing

10.1016/j.jprot.2020.103986 · 2021 · External reference

Not a limitless resource: ethics and guidelines for destructive sampling of archaeofaunal remains

10.1098/rsos.191059 · 2019 · External reference

Ethical sampling guidance

2019 · External reference

Unresolved reference

2023 · External reference

Assessing the degradation of ancient milk proteins through site-specific deamidation patterns

10.1038/s41598-021-87125-x · 2021 · External reference

DeamiDATE 1.0: Site-specific deamidation as a tool to assess authenticity of members of ancient proteomes

10.1016/j.jas.2020.105080 · 2020 · External reference

Fossils from conflict zones and reproducibility of fossil-based scientific data.

2020 · External reference

CARE Principles

2019 · External reference

A primer for ZooMS applications in archaeology

10.1073/pnas.2109323119 · 2022 · External reference

Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins

10.24072/pcjournal.491 · 2024 · External reference

Dual DNA-protein extraction from human archeological remains

10.1007/s12520-018-0760-1 · 2019 · External reference

SPIN enables high throughput species identification of archaeological bone by proteomics

10.1038/s41467-022-30097-x · 2022 · External reference

Non-avian dinosaur eggshell calcite can contain ancient, endogenous amino acids

10.1016/j.gca.2023.11.016 · 2024 · External reference

Toward a conceptual framework for assessing the human dimensions of paleontological resources

2016 · External reference

Proteomic profiling of archaeological human bone

10.1098/rsos.161004 · 2017 · External reference

Glutamine deamidation: an indicator of antiquity, or preservational quality?

10.1002/rcm.7445 · 2016 · External reference

Expansion for the Brachylophosaurus canadensis Collagen I Sequence and Additional Evidence of the Preservation of Cretaceous Protein

10.1021/acs.jproteome.6b00873 · 2017 · External reference

Exotic foods reveal contact between South Asia and the Near East during the second millennium BCE

10.1073/pnas.2014956117 · 2021 · External reference

Emergence and intensification of dairying in the Caucasus and Eurasian steppes

10.1038/s41559-022-01701-6 · 2022 · External reference

Ancient Proteins Extraction Protocol

2020 · External reference

Identifying the unidentified fauna enhances insights into hominin subsistence strategies during the Middle to Upper Palaeolithic transition

10.1007/s12520-023-01830-4 · 2023 · External reference

Combining ZooMS and zooarchaeology to study Late Pleistocene hominin behaviour at Fumane (Italy)

10.1038/s41598-019-48706-z · 2019 · External reference

Identification and tentative removal of collagen glue in Palaeolithic worked bone objects: implications for ZooMS and radiocarbon dating

10.1038/s41598-023-49242-7 · 2023 · External reference

Member Bylaw on Ethics Statement

2025 · External reference

Initial evidence of research quality of registered reports compared with the standard publishing model

10.1038/s41562-021-01142-4 · 2021 · External reference

Chasing the elusive viscacha in Precolumbian textiles at the intersection of art and science

10.1016/j.jas.2022.105575 · 2022 · External reference

Modeling deamidation in sheep α-keratin peptides and application to archeological wool textiles

10.1021/ac4026362 · 2014 · External reference

Enhanced Global Post-translational Modification Discovery with MetaMorpheus

10.1021/acs.jproteome.7b00873 · 2018 · External reference

Collaborate equitably in ancient DNA research and beyond

10.1038/d41586-021-03541-z · 2021 · External reference

Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans

10.1098/rstb.2015.0332 · 2016 · External reference

Shortcut citations in the methods section: Frequency, problems, and strategies for responsible reuse

10.1371/journal.pbio.3002562 · 2024 · External reference

Sex determination of human remains from peptides in tooth enamel

10.1073/pnas.1714926115 · 2017 · External reference

Mass spectrometrists should search for all peptides, but assess only the ones they care about

10.1038/nmeth.4338 · 2017 · External reference

mMass 3: a cross-platform software environment for precise analysis of mass spectrometric data

10.1021/ac100818g · 2010 · External reference

Rules governing protein identification by mass spectrometry

10.1002/rcm.2225 · 2005 · External reference

The York Gospels: a 1000-year biological palimpsest

10.1098/rsos.170988 · 2017 · External reference

Highly accurate protein structure prediction for the human proteome

10.1038/s41586-021-03828-1 · 2021 · External reference

Palaeoproteomics and ZooMS

2025 · External reference

Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows

10.1038/s41467-021-27542-8 · 2021 · External reference

The dental calculus metabolome in modern and historic samples

10.1007/s11306-017-1270-3 · 2017 · External reference

Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra

10.1038/nmeth705 · 2004 · External reference

Clothomics: a practical guide to understand the opportunities and challenges of omics-based methods in archaeological cloth research

10.1038/s40494-025-01623-z · 2025 · External reference

A biological reading of a palimpsest

10.1016/j.isci.2023.106786 · 2023 · External reference

SpecieScan: Semi-Automated taxonomic identification of bone collagen peptides from MALDI-ToF MS spectra

10.1093/bioinformatics/btae054 · 2024 · External reference

Direct evidence of milk consumption from ancient human dental calculus

10.1038/srep07104 · 2014 · External reference

Paleoproteomics

10.1021/acs.chemrev.1c00703 · 2022 · External reference

Pathogens and host immunity in the ancient human oral cavity

10.1038/ng.2906 · 2014 · External reference

Amino acids in fossil corals: racemization (epimerization) reactions and their implications for diagenetic models and geochronological studies

10.1016/0016-7037(76)90029-6 · 1976 · External reference

Ancient proteins resolve the evolutionary history of Darwin's South American ungulates

10.1038/nature14249 · 2015 · External reference

Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne

10.1073/pnas.1605834113 · 2016 · External reference

The dental proteome of Homo antecessor

10.1038/s41586-020-2153-8 · 2020 · External reference

10.1007/978-0-387-98141-3

10.1007/978-0-387-98141-3 · 2009 · External reference

Sequential trypsin and ProAlanase digestions unearth immunological protein biomarkers shrouded by skeletal collagen

10.1016/j.isci.2024.109663 · 2024 · External reference

Dairying enabled Early Bronze Age Yamnaya steppe expansions

10.1038/s41586-021-03798-4 · 2021 · External reference

The FAIR Guiding Principles for scientific data management and stewardship

10.1038/sdata.2016.18 · 2016 · External reference

Assessing the extent of bone degradation using glutamine deamidation in collagen

10.1021/ac301333t · 2012 · External reference

Grouping groupers in the Mediterranean: Ecological baselines revealed by ancient proteins

10.1002/ece3.10625 · 2023 · External reference

Middle and Late Pleistocene Denisovan subsistence at Baishiya Karst Cave

10.1038/s41586-024-07612-9 · 2024 · External reference

PEAKS DB: de novo sequencing assisted database search for sensitive and accurate peptide identification

10.1074/mcp.m111.010587 · 2012 · External reference