4.8 Review

Paleoproteomics

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Article Biochemical Research Methods

Recent progress in the analysis of protein deamidation using mass spectrometry

Yujia Ying et al.

Summary: Deamidation is a nonenzymatic and spontaneous posttranslational modification that is strongly associated with aging proteome instability and degenerative diseases. It is also a major cause of degradation in biopharmaceutical proteins. Mass spectrometry analysis is an important tool for accurate characterization of protein deamidation and its related modifications, providing insights into disease pathology and drug development.

METHODS (2022)

Article Archaeology

Medieval Whalers in the Netherlands and Flanders: Zooarchaeological Analysis of Medieval Cetacean Remains

Youri van den Hurk et al.

Summary: Medieval historical sources reveal that whale exploitation was mainly reserved for the social elite in Europe, including the Netherlands and Flanders. However, the frequency of active hunting and the targeted species remains uncertain. By using zooarchaeological techniques, cetacean remains from Medieval sites in the Netherlands and Flanders were identified to the species level, showing that North Atlantic right whales, sperm whales, and grey whales were commonly exploited. Active whaling activities were particularly prominent in Flanders and Frisia. These findings confirm the historical evidence that the social elite had a preference for cetacean meat, as evidenced by the presence of cetacean remains in high-status sites such as castles and ecclesiastical locations. However, cetacean products were also accessible outside elite and ecclesiastical contexts.

ENVIRONMENTAL ARCHAEOLOGY (2022)

Article Biochemistry & Molecular Biology

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

Yasset Perez-Riverol et al.

Summary: PRIDE is the largest data repository of mass spectrometry-based proteomics data in the world, with around 500 datasets submitted per month. In addition to continuous improvements in data pipelines and infrastructure, PRIDE has developed the Spectra Archive and MAGE-TAB file format to enhance sample metadata annotation and access to mass spectra.

NUCLEIC ACIDS RESEARCH (2022)

Article Multidisciplinary Sciences

Linking protein structural and functional change to mutation using amino acid networks

Cristina Sotomayor-Vivas et al.

Summary: The study investigates the relationship between protein structure and function, revealing a strong correlation between structural changes and functional changes. Significant changes in protein structure are associated with functional loss, while positions that gain function through mutations tend to be structurally robust. A computational method is also proposed to predict mutation-sensitive positions using structural changes, demonstrating good predictive performance.

PLOS ONE (2022)

Article Multidisciplinary Sciences

Sequence locally, think globally: The Darwin Tree of Life Project

Mark L. Blaxter

Summary: The Earth Biogenome Project aims to sequence the genomes of all eukaryotic life on earth, and the Darwin Tree of Life Project focuses on delivering high-quality genome sequences for the British and Irish islands. The collaboration between biodiversity organizations and genomics institutes has established a workflow that collects specimens, performs sequencing, generates curated assemblies, and openly releases the data for global use in future scientific and conservation efforts.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

Article Multidisciplinary Sciences

A primer for ZooMS applications in archaeology

Kristine Korzow Richter et al.

Summary: Collagen peptide mass fingerprinting by MALDI-TOF-MS, also known as ZooMS, is a rapidly growing analytical technique in the fields of archaeology, ecology, and cultural heritage. It enables rapid taxonomic identification of large bone assemblages and cultural heritage objects. However, there are limitations that need to be addressed for future advancements.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

Article Multidisciplinary Sciences

SPIN enables high throughput species identification of archaeological bone by proteomics

Patrick Leopold Ruther et al.

Summary: The authors developed a workflow called Species by Proteome INvestigation (SPIN) for analyzing archaeological bone using liquid chromatography-tandem mass spectrometry, which is capable of identifying over 150 mammalian species with automated sample preparation and faster data acquisition. The SPIN method was successfully validated in both known reference bones and blind tests of Iron-Age material from Scandinavia, demonstrating its reproducibility and high throughput capabilities. This new method has the potential to expand to other biological tissues and taxa in the future.

NATURE COMMUNICATIONS (2022)

Article Anthropology

The last meal of Tollund Man: new analyses of his gut content

Nina H. Nielsen et al.

Summary: The last meal of Tollund Man consisted of barley, pale persicaria, flax, and possibly fish, eaten 12-24 hours before his death, with evidence of parasitic infection. The inclusion of threshing waste in the meal could be related to ritual practices, shedding new light on life and death in the Danish Early Iron Age through modern analytical techniques.

ANTIQUITY (2021)

Article Biochemical Research Methods

Relative Protein Abundances and Biological Ageing in Whole Skeletal Elements

Elizabeth Johnston et al.

Summary: Establishing biological age is crucial in forensic investigations, with biomolecular approaches considered of great interest. A study using a rat model to evaluate the proteome of complete skeletal elements identified potential new protein markers for age estimation.

JOURNAL OF PROTEOME RESEARCH (2021)

Review Biochemistry & Molecular Biology

Imaging the future: the emerging era of single-cell spatial proteomics

Indranil Paul et al.

Summary: The proteome of a human cell is compartmentalized within organelles and subcellular compartments, allowing for efficient biochemical processes and protein localization. Proper delivery and dynamic exchange of proteins between compartments regulate cellular processes, while mis-localization can lead to pathology. Single-cell measurements are essential due to variations in protein expression, modification, and associations, which can result in biological heterogeneity.

FEBS JOURNAL (2021)

Article Archaeology

Finding of muscle proteins in art samples from mid-18th century murals by LC-MSMS

Ivana K. Levy et al.

Summary: This study used a proteomic approach to analyze protein binders in micro-samples from mural paintings of two 18th century Colonial Andean churches in northern Chile. Collagen, egg white and yolk proteins were identified, along with the presence of muscle proteins in two samples for the first time. The findings offer new insights into the composition of old animal glues and painting practices in the Andean region.

JOURNAL OF CULTURAL HERITAGE (2021)

Article Biochemical Research Methods

Tailoring to Search Engines: Bottom-Up Proteomics with Collision Energies Optimized for Identification Confidence

Agnes Revesz et al.

Summary: Bottom-up proteomics relies on identifying peptides from tandem mass spectra using sequence databases. Changes in collision energy affect identification scores for different search engines, impacting protein identification and coverage. Adjusting experimental parameters based on the choice of engine can optimize results.

JOURNAL OF PROTEOME RESEARCH (2021)

Article Biochemical Research Methods

Mass-Spectrometry-Based Near-Complete Draft of the Saccharomyces cerevisiae Proteome

Yuan Gao et al.

Summary: Proteomics approaches have developed in recent years to catalog all open reading frames (ORFs) under a defined set of growth conditions, but no proteome has been completely sequenced so far. This study presents the largest yeast proteome data set to date, with 5610 identified proteins, achieving near-complete coverage of yeast ORFs. The comprehensive analysis of missing proteins revealed that physical properties are the main reason for protein omission, and the protein abundance highly correlates with mRNA abundance, demonstrating a high level of accuracy, sensitivity, and precision in the data. The near-complete yeast proteome data set will serve as a valuable resource for further systematic studies.

JOURNAL OF PROTEOME RESEARCH (2021)

Article Biochemical Research Methods

Diagenetiforms: A new term to explain protein changes as a result of diagenesis in paleoproteomics

Timothy P. Cleland et al.

Summary: The term "diagenetiform" is introduced to accurately describe the changes detected on ancient proteins due to burial, providing a new opportunity for top-down paleoproteomic studies.

JOURNAL OF PROTEOMICS (2021)

Article Biochemical Research Methods

Taxonomic identification of Danish Viking Age shoes and skin objects by ZooMS (Zooarchaeology by mass spectrometry)

Luise Orsted Brandt et al.

JOURNAL OF PROTEOMICS (2021)

Article Biochemical Research Methods

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

Clara Azemard et al.

Summary: This study provides a novel approach combining proteomic analysis to differentiate South American camelid species, offering discriminant features for the determination of species of origin. By analyzing peptides specific to different SAC species, the study contributes valuable information for archaeozoology and fraud control.

JOURNAL OF PROTEOMICS (2021)

Article Biochemical Research Methods

A versatile and user-friendly approach for the analysis of proteins in ancient and historical objects

Georgia Ntasi et al.

Summary: The enzyme functionalized films described in this study can efficiently analyze a variety of ancient objects. The captured digested peptides on the functionalized surface are suitable for LC-MS/MS analysis, and a deglycosylation pretreatment can improve the detection of glycosylated proteins. These trypsin functionalized films offer a user-friendly and versatile tool for the diagnosis of cultural heritage objects, ancient proteins, and palaeoproteomics.

JOURNAL OF PROTEOMICS (2021)

Article Multidisciplinary Sciences

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

Ashley Scott et al.

Summary: By analyzing microremains and proteins preserved in dental calculus from individuals in the Southern Levant during the second millennium BCE, it has been found that people in the Eastern Mediterranean had access to food from distant locations such as South Asia, including soybean, banana, and turmeric, pushing back the earliest evidence of these foods in the Mediterranean by centuries or even millennia. This challenges previous perceptions of the complexity and intensity of Indo-Mediterranean trade during the Bronze Age and the degree of globalization in early Eastern Mediterranean cuisine.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Article Geography, Physical

The Mammuthus-Coelodonta Faunal Complex at its southeastern limit: A biogeochemical paleoecology investigation in Northeast Asia

Jiao Ma et al.

Summary: This study investigates the paleoecology of the Mammuthus-Coelodonta Faunal Complex in Northeast Asia through radiocarbon dating, ZooMS, and stable isotope analysis. The research reveals dietary habits and adaptability of megaherbivores like the woolly mammoth, woolly rhinoceros, and steppe bison in the region. Additionally, the study highlights the unique scenario of this biome in Northeast Asia and emphasizes the need for more systematic studies in and outside this region.

QUATERNARY INTERNATIONAL (2021)

Article Biochemical Research Methods

Proteomic profile of bone collagen extracted for stable isotopes: Implications for bulk and single amino acid analyses

Timothy P. Cleland et al.

Summary: Proteomic techniques have provided a more comprehensive understanding of protein diagenesis in archaeology and paleontology, revealing various proteins in addition to collagen. The correlation between total deamidation and wt% N suggests a potential impact on nitrogen signal in bulk analyses. Despite varying sample quality, the amino acid profiles still reflect expected collagen I percentages, allowing for valid single amino acid stable isotope analyses.

RAPID COMMUNICATIONS IN MASS SPECTROMETRY (2021)

Article Multidisciplinary Sciences

Ancient proteins provide evidence of dairy consumption in eastern Africa

Madeleine Bleasdale et al.

Summary: The consumption of milk from other species is a unique adaptation of Homo sapiens, with evidence of milk consumption in ancient Africa at least six millennia ago. Analysis of dental calculus from 41 ancient individuals from Sudan and Kenya shows that milk consumption occurred as soon as herding spread into eastern Africa.

NATURE COMMUNICATIONS (2021)

Article Anthropology

Proteomics analysis of the soil textile imprints from tomb M6043 of the Dahekou Cemetery site in Yicheng County, Shanxi Province, China

Li Li et al.

Summary: Proteomics has been crucial in identifying ancient protein residues, particularly in analyzing severely degraded archeological remains. This study used liquid chromatography-tandem mass spectrometry to determine that the textile imprints from tomb M6043 in the Dahekou Cemetery site were silk fiber residues. These findings demonstrate the potential of proteomics in studying archeological protein residues and the significance of textile soil imprints as archaeological materials for ancient textile research.

ARCHAEOLOGICAL AND ANTHROPOLOGICAL SCIENCES (2021)

Review Multidisciplinary Sciences

Ancient protein analysis in archaeology

Jessica Hendy

Summary: Ancient protein analysis offers insights into past subsistence practices, health patterns, evolution, and environments, with the review tracking its development and discussing challenges faced by the field. Future directions include developing minimally invasive techniques, enhancing protein authentication strategies, and integrating ancient protein analysis with other biomolecular techniques.

SCIENCE ADVANCES (2021)

Article Multidisciplinary Sciences

Trabecular bone organoid model for studying the regulation of localized bone remodeling

Yongkuk Park et al.

Summary: A tissue-engineered model is described that replicates bone tissue complexity and remodeling processes, allowing for further investigation into trabecular bone niche biology.

SCIENCE ADVANCES (2021)

Review Biochemistry & Molecular Biology

AlphaFold and the amyloid landscape

Francisca Pinheiro et al.

Summary: Protein aggregation is a widespread phenomenon with functional amyloids playing important roles in physiology, while structural details of most amyloidogenic species remain elusive.

JOURNAL OF MOLECULAR BIOLOGY (2021)

Review Archaeology

A comprehensive review on moth repellent finishing of woolen textiles

Kumari Medha et al.

Summary: This paper discusses the insect infestation issues faced by wool fibers, various control methods, and the effectiveness of herbal and chemical mothproofing agents. It emphasizes the urgent need to promote natural mothproofing agents for effective management of textile pests.

JOURNAL OF CULTURAL HERITAGE (2021)

Article Biochemical Research Methods

Comparing the Use of Magnetic Beads with Ultrafiltration for Ancient Dental Calculus Proteomics

Karren S. Palmer et al.

Summary: This study compared traditional methods and new methods in recovering proteomes from ancient dental calculus, finding that a protocol utilizing EDTA combined with paramagnetic beads increased proteome complexity and diversity. The increase in proteins was mainly of bacterial origin, which has implications for studying diseases in ancient populations.

JOURNAL OF PROTEOME RESEARCH (2021)

Article Biochemical Research Methods

Proteome Variation with Collagen Yield in Ancient Bone

Noemi Procopio et al.

Summary: Isotope analyses are common in analyzing ancient bones for diet and chronology interpretation. Evaluating collagen yield is important for selecting adequate specimens, and this study used proteomic methods to investigate proteinaceous biomolecules in poorly preserved samples. While waste fractions contain significant proteins, their abundance does not correlate with collagen yield, suggesting they can still provide useful molecular information.

JOURNAL OF PROTEOME RESEARCH (2021)

Article Biochemical Research Methods

On the standardization of ZooMS nomenclature

Samantha Brown et al.

Summary: ZooMS, a peptide mass fingerprinting technique, is increasingly utilized in archaeological and cultural heritage science, but faces challenges due to inconsistent nomenclature for peptide markers. Standardized guidelines proposed here aim to provide a reliable and consistent naming system, supporting the growth of ZooMS across diverse vertebrate taxa.

JOURNAL OF PROTEOMICS (2021)

Review Biochemical Research Methods

New baits for fishing in cultural heritage's Mare Magnum

Pier Giorgio Righetti et al.

Summary: EVA is a modern tool for exploring Cultural Heritage documents, avoiding contamination or damage. It can collect and analyze various surface materials, and detect traces of famous authors and paintings.

JOURNAL OF PROTEOMICS (2021)

Article Biochemical Research Methods

Testing the efficacy and comparability of ZooMS protocols on archaeological bone

Wang Naihui et al.

Summary: This study compares three different ZooMS protocols and finds that acid-based methods can improve success rates for bones with low to medium collagen preservation, while the least-destructive protocol using ammonium bicarbonate buffer is suitable for well-preserved bones. By utilizing 0.26% N as a threshold, the number of samples with enough collagen for successful peptide mass fingerprinting can be optimized.

JOURNAL OF PROTEOMICS (2021)

Article Multidisciplinary Sciences

A novel route for identifying starch diagenetic products in the archaeological record

Thomas Oldenburg et al.

Summary: This study introduces a new analytical chemistry method for studying archaeological starch residues, utilizing laboratory synthesis of model Maillard reaction mixtures and analysis through FTICR-MS. The analysis revealed over 5,300 molecular compounds and identified a range of unique compound classes, providing insights into the origin and process-specific characteristics of starch. The research highlights the potential of FTICR-MS in characterizing starchy residue and recognizing taxonomic signals in fossil contexts.

PLOS ONE (2021)

Article Multidisciplinary Sciences

Million-year-old DNA sheds light on the genomic history of mammoths

Tom van der Valk et al.

Summary: This study reveals the presence of two distinct mammoth lineages in eastern Siberia during the Early Pleistocene, with one lineage giving rise to the woolly mammoth and another representing an unrecognized lineage ancestral to the first mammoths to colonize North America. Additionally, the study shows that the Columbian mammoth of North America can trace its ancestry back to a hybridization event between these two lineages during the Middle Pleistocene, with roughly equal admixture proportions. Moreover, the majority of protein-coding changes associated with cold adaptation in woolly mammoths were found to be present as early as one million years ago.

NATURE (2021)

Article Multidisciplinary Sciences

Creation of a peptide database of corneous beta-proteins of marine turtles for the identification of tortoiseshell: archaeological combs as case study

Caroline Solazzo et al.

Summary: Tortoiseshell, a proteinaceous material derived from marine turtles, was used to create luxurious items in the 17th and 18th centuries and continues to drive illegal poaching of marine turtles. Proteomics analysis has identified marker sequences that can be used for species identification and studying degradation patterns in archaeological tortoiseshell.

ROYAL SOCIETY OPEN SCIENCE (2021)

Article Multidisciplinary Sciences

Girding the loins? Direct evidence of the use of a medieval English parchment birthing girdle from biomolecular analysis

Sarah Fiddyment et al.

Summary: This study successfully extracted proteins from a medieval birth girdle using advanced techniques, revealing evidence of the use of honey, cereals, ovicaprine milk, and legumes, as well as a significant number of human peptides indicating active use during childbirth.

ROYAL SOCIETY OPEN SCIENCE (2021)

Editorial Material Food Science & Technology

Proteomics and Food Analysis: Principles, Techniques, and Applications

Monica Carrera

Article Biochemical Research Methods

Ancient enamel peptides recovered from the South American Pleistocene species Notiomastodon platensis and Myocastor cf. coypus

Fabio C. S. Nogueira et al.

Summary: This study used fossil teeth from South American Pleistocene mammals to recover ancient peptides from subsuperficial enamel, primarily enamel-specific proteins. The research suggests that peptides are likely the best preserved biomolecules under certain harsh environmental conditions. The procedure for obtaining these peptides was minimally destructive to the fossils and opens up new possibilities for the study of the past.

JOURNAL OF PROTEOMICS (2021)

Article Biochemical Research Methods

Novel Strategies to Address the Challenges in Top-Down Proteomics

Jake A. Melby et al.

Summary: Top-down proteomics is a powerful technology for comprehensively characterizing proteoforms and understanding protein functions, disease mechanisms, and biomarkers. However, challenges in protein solubility, data analysis, and proteome complexity remain. Recent technological developments include the development of new surfactants, nanoparticles for enriching proteoforms, and strategies for multi-dimensional chromatography separation of proteins.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2021)

Article Multidisciplinary Sciences

Towards complete and error-free genome assemblies of all vertebrate species

Arang Rhie et al.

Summary: The Vertebrate Genome Project and the international Genome 10K consortium have collaborated to generate high-quality genome assemblies for 16 species representing six major vertebrate lineages, leading to new biological discoveries. Long-read sequencing technologies are essential for maximizing genome quality, and addressing complex repeats and haplotype heterozygosity are crucial for reducing assembly errors and improving completeness of reference genomes. The lessons learned from this project have paved the way for the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all known vertebrate species.

NATURE (2021)

Article Multidisciplinary Sciences

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

Anneke Janzen et al.

Summary: This study provides a complete set of ZooMS peptide markers for African bovid tribes and identifies two novel peptide markers for further distinguishing between bovid groups. The results demonstrate that nearly all African bovid subfamilies can be distinguished using ZooMS methods, revealing greater taxonomic richness than morphology-based analyses.

PLOS ONE (2021)

Article Multidisciplinary Sciences

Palaeoproteomics confirm earliest domesticated sheep in southern Africa ca. 2000 BP

Ashley N. Coutu et al.

Summary: Using palaeoproteomics and peptide mass fingerprinting, this study identified key specimens of early domesticated fauna from South Africa, successfully distinguishing between sheep and wild bovids and confirming the earliest evidence of domesticated animals in southern Africa. The research highlights the importance of developing regional frameworks for biomolecular species identification using Zooarchaeology by Mass Spectrometry.

SCIENTIFIC REPORTS (2021)

Article Multidisciplinary Sciences

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

Abigail Ramsoe et al.

Summary: This study examines the use of site-specific deamidation rates in identifying modern contamination and authenticating ancient milk proteins, showing its potential but also highlighting the challenges posed by the high variability of deamidation rates in ancient milk peptides. Multiple lines of evidence are needed to authenticate ancient protein data due to this variability.

SCIENTIFIC REPORTS (2021)

Review Genetics & Heredity

Evolution of the Avian Eggshell Biomineralization Protein Toolkit - New Insights From Multi-Omics

Nathalie Le Roy et al.

Summary: The avian eggshell is a unique biomineral made of 95% calcite and 3.5% organic matrix, which plays a crucial role in protecting the egg contents and facilitating embryonic development. Advancements in high-throughput technologies have allowed researchers to identify key proteins involved in eggshell biomineralization, enhancing our understanding of this complex process in birds.

FRONTIERS IN GENETICS (2021)

Article Humanities, Multidisciplinary

Scratching the surface: the use of sheepskin parchment to deter textual erasure in early modern legal deeds

Sean Paul Doherty et al.

Summary: Historic legal deeds, abundant in British archives, are often neglected. Research shows that sheepskin parchment was preferentially used from the 16th to 20th centuries, possibly due to its unique structure enhancing visibility of fraudulent text modification.

HERITAGE SCIENCE (2021)

Article Humanities, Multidisciplinary

A comparative study on the extraction effects of common agents on collagen-based binders in mural paintings

Jianghao Du et al.

Summary: This study conducted a comparative investigation on the extraction effects of six agents for collagen-based mural painting binders. It was found that 2 M guanidine hydrochloride (GuHCl) exhibited significantly higher extraction efficiency with less damage to the protein structure compared to the other agents for both non-aged and aged samples.

HERITAGE SCIENCE (2021)

Article Physics, Atomic, Molecular & Chemical

Exploring frontiers of orbitrap performance for long transients

Eduard Denisov et al.

Summary: Experiments on a modified Orbitrap Exploris instrument have demonstrated that a resolving power in excess of 2,000,000 can be achieved even in a compact instrument when appropriate tolerance and tuning requirements are met. Improved pumping design in a new Orbitrap allows isotopic resolution of intact monoclonal antibodies, with longer transients improving signal-to-noise ratios towards single-charge resolution levels in charge detection mass spectrometry. Further steps for enhancing instrumentation are discussed.

INTERNATIONAL JOURNAL OF MASS SPECTROMETRY (2021)

Article Anthropology

Sex estimation based on the analysis of enamel peptides: False assignments due to AMELY deletion

Iztok Stamfelj

Summary: The proteomic analysis of sex-specific amelogenin peptides in tooth enamel is a promising method for sex determination in human skeletal remains, but it has limitations due to technical issues and AMELY gene deletion, which may lead to misidentification of sex.

JOURNAL OF ARCHAEOLOGICAL SCIENCE (2021)

Article Anthropology

Iron Age hunting and herding in coastal eastern Africa: ZooMS identification of domesticates and wild bovids at Panga ya Saidi, Kenya

Courtney Culley et al.

Summary: The study utilized ZooMS to identify domesticates and wild bovids in Iron Age assemblages at Panga ya Saidi in southeast Kenya, providing critical evidence for the use of domesticates by resident foraging populations during the period associated with the arrival of food production in coastal Kenya. The results also demonstrate the persistence of hunting and the secondary role of acquiring livestock in hunter-gatherer foodways during the introduction of agro-pastoralism.

JOURNAL OF ARCHAEOLOGICAL SCIENCE (2021)

Editorial Material Anthropology

AMELY deletion is not detected in systematically sampled reference populations: A Reply to Stamfelj

Glendon J. Parker et al.

Summary: Biomolecular sex estimation using genomic and proteomic methods is a valuable tool in bioarchaeology, but has limitations and challenges that need to be addressed. Proteomic sex estimation based on amelogenin protein fragments in enamel is sensitive and quantifiable. Structural variants of the Y-chromosome and low peptide signals in mass spectrometry may complicate sex estimation results.

JOURNAL OF ARCHAEOLOGICAL SCIENCE (2021)

Article Anthropology

Examining collagen preservation through glutamine deamidation at Denisova Cave

Samantha Brown et al.

Summary: The use of glutamine deamidation to measure decay in archaeological bones has been controversial, with growing evidence suggesting no reliable link between deamidation and chronological age. A study on fossils from Denisova Cave shows high intra and inter layer variability, cautioning against linking deamidation with decay or age.

JOURNAL OF ARCHAEOLOGICAL SCIENCE (2021)

Article Biology

Palaeoproteomic analyses of dog palaeofaeces reveal a preserved dietary and host digestive proteome

Anne Kathrine W. Runge et al.

Summary: This study utilized zooarchaeology by mass spectrometry and liquid chromatography tandem mass spectrometry to analyze dog palaeofaeces from the Nunalleq site, Alaska, revealing that the material can recover gastrointestinal proteomes and showing that the diet of the Nunalleq dogs primarily consisted of various Pacific salmon species.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2021)

Article Multidisciplinary Sciences

Zooarchaeology through the lens of collagen fingerprinting at Denisova Cave

Samantha Brown et al.

Summary: Denisova Cave in the Altai Mountains of Russian Siberia has provided significant fossil evidence for the Pleistocene in Northern Asia. Through ZooMS analysis of bone fragments, trends related to climate variability and patterns of bone fragmentation have been identified, indicating a cyclical pattern involving human-induced and carnivore-related fragmentation.

SCIENTIFIC REPORTS (2021)

Article Multidisciplinary Sciences

A biocodicological analysis of the medieval library and archive from Orval Abbey, Belgium

Nicolas Ruffini-Ronzani et al.

Summary: The analysis of parchments from manuscript books and archives in the Orval Abbey revealed a balanced use of calfskin and sheepskin in internal production, with calfskin being preferred for higher quality manuscripts. In externally acquired units, calfskin was less frequent. This suggests a difference in production patterns between archival documents and library books.

ROYAL SOCIETY OPEN SCIENCE (2021)

Article Anthropology

Adaptive Trade-offs Towards the Last Glacial Maximum in North-Western Europe: a Multidisciplinary View from Walou Cave

Luc Moreau et al.

Summary: The impact of deteriorating climatic conditions on the variability in archaeological record prior to the Last Glacial Maximum remains uncertain. This study investigates the Gravettian technological organization compared to the previous Aurignacian based on two assemblages from Walou Cave, Belgium, to understand the adaptive trade-offs brought about by the general climatic downturn towards the Last Glacial Maximum in North-Western Europe. The results suggest that Gravettian technologies are unlikely to solely be a product of heightened risk in relation to significant reshuffling of food resources compared to the previous Aurignacian.

JOURNAL OF PALEOLITHIC ARCHAEOLOGY (2021)

Article Archaeology

Potential applications of biomolecular archaeology to the ecohistory of sea turtles and groupers in Levant coastal antiquity

Rachel M. Winter et al.

Summary: Humans have been exploiting marine resources along the Levantine coast for thousands of years. Advances in biomolecular archaeology, such as collagen peptide fingerprinting, ancient DNA analysis, and stable isotope analysis, offer new opportunities to understand the exploitation of specific species. By combining biomolecular archaeology with traditional zooarchaeological techniques, researchers can further investigate human impacts on marine ecosystems.

JOURNAL OF ARCHAEOLOGICAL SCIENCE-REPORTS (2021)

Review Multidisciplinary Sciences

Bayesian statistics and modelling

Rens van de Schoot et al.

Summary: Bayesian statistics is a data analysis approach based on Bayes' theorem, which involves determining parameters through prior distributions, likelihood functions, and posterior distributions. This method has shown successful applications in various disciplines and has improved accuracy in predicting future events.

NATURE REVIEWS METHODS PRIMERS (2021)

Article Biochemistry & Molecular Biology

Ensembl 2021

Kevin L. Howe et al.

Summary: The Ensembl project provides genome annotation and data dissemination services for vertebrate species, including detailed annotation of gene structures, regulatory elements, and variants, as well as inferring the evolutionary history of genes and genomes. They offer integrated genomic data through various means such as genome browsers, search interfaces, specialist tools, and download files. Recent developments include the Ensembl Rapid Release and the SARS-CoV-2 genome browser, aiding in the international scientific response to the COVID-19 pandemic.

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DeepMSPeptide: peptide detectability prediction using deep learning

Guillermo Serrano et al.

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Art-omics: multi-omics meet archaeology and art conservation

Cristina Vilanova et al.

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The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics

Eric W. Deutsch et al.

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In situ mass spectrometry analysis of intact proteins and protein complexes from biological substrates

Oliver J. Hale et al.

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

Abigail Ramsoe et al.

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Flame retardant cellulosic fabrics via layer-by-layer self-assembly double coating with egg white protein and phytic acid

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Protein aggregate formation permits millennium-old brain preservation

Axel Petzold et al.

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Multi-omics approaches to human biological age estimation

Ilya Solovev et al.

MECHANISMS OF AGEING AND DEVELOPMENT (2020)

Editorial Material Biotechnology & Applied Microbiology

Reading amino acids in a nanopore

Stefan Howorka et al.

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Letter Medicine, General & Internal

Heat-Induced Brain Vitrification from the Vesuvius Eruption in CE 79

Pierpaolo Petrone et al.

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The role of birds at Çatalhöyük revealed by the analysis of eggshell

Beatrice Demarchi et al.

QUATERNARY INTERNATIONAL (2020)

Review Biochemistry & Molecular Biology

Strategies for Development of a Next-Generation Protein Sequencing Platform

Nicholas Callahan et al.

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Beyond mass spectrometry, the next step in proteomics

Winston Timp et al.

SCIENCE ADVANCES (2020)

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Dairy pastoralism sustained eastern Eurasian steppe populations for 5,000 years

Shevan Wilkin et al.

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

Simon Hickinbotham et al.

BIOINFORMATICS (2020)

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The what, how and why of archaeological coprolite analysis

Lisa-Marie Shillito et al.

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What's the catch? Archaeological application of rapid collagen-based species identification for Pacific Salmon

Kristine Korzow Richter et al.

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Article Multidisciplinary Sciences

Molecular and isotopic evidence for milk, meat, and plants in prehistoric eastern African herder food systems

Katherine M. Grillo et al.

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