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

Paleoproteomic identification of the species used in fourteenth century gut-skin garments from the archaeological site of Nuulliit, Greenland

Until recently, the identification of the species of origin for skin and fur materials used in the production of archaeological clothing has been based on the analysis of macro- and microscopic morphological features and on the traditional knowledge of Indigenous groups. This approach, however, is not always applicable due to the deterioration of the archaeological objects. Paleoproteomics was used as an alternative approach to identify the species of origin of fifteen samples of various tissues from approximately 600-year-old garments found in Nuulliit, northern Greenland. Proteomics revealed that a limited group of marine and terrestrial mammals were used for clothing production. The results obtained from the analysis of multiple types of clothing and elements, such as sinew thread and gut skin, suggest that their applications were based on their properties. When conclusive assignment of a sample to a species via proteomics was not possible, the observation by transmitted light microscopy of feather and hair micromorphology, if not affected by diagenesis, was used to improve the identification. The proteomic characterization of animal materials used for clothing production in the Nuulliit archaeological context provides an insight into the practical knowledge and the strategies adopted by the local Indigenous community to exploit natural resources.

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

Two distemper paint samples taken from decorative boards in Uvdal stave church, Norway, were analysed using palaeoproteomics, with an aim of identifying their binder and possible contaminants. The results point at the use of calfskin to produce hide glue as the original paint binder, and are consistent with the instructions of binder production and resource allocation in the historical records of Norway. Although we did not observe any evidence of prior restoration treatments using protein-based materials, we found abundant traces of human saliva proteins, as well as a few oats and barley peptides, likely deposited together on the boards during their discovery in the 1970s. This work illustrates the need to fully consider contamination sources in palaeoproteomics and to inform those working with such objects about the potential for their contamination.

Palaeoproteomics and microanalysis reveal techniques of production of animal-based metal threads in medieval textiles

Animal-based metal threads were largely used between the 10th and the fifteenth century, in European, Middle Eastern and Far Eastern textile productions for the decoration of textiles and cloths. They belong to a larger group of metal threads, used either as flat threads or wrapped around a fiber core, that were backed by an organic support (animal or paper). This study focuses on the medieval production of metal threads backed by an animal membrane (e.g. gut membrane), or skin. A total of 91 samples were collected from a corpus of 66 textile fragments belonging to 54 catalogued objects. The relevance and novelty of the present study is represented by the combination of proteomics, cross-section analysis, and scanning electron microscopy (SEM-EDS and SEM-µXRF). The diversity of materials and manufacturing techniques found within each typology of thread, respectively, membrane-based metal threads and skin-based metal threads, hinted at different production technologies. Membrane-based threads were found to be invariably made from cattle gut membrane, coated with gilt-silver leaves. A possible sheep glue adhesive was found in a few samples. Skin-based threads were made from either goat or sheep leather, coated with metal leaves or powder. Within the three different types of coatings identified (silver, gold and gilt-silver), gold coatings were the most represented. Goat leather threads were associated with an egg-white binder, while sturgeon glue was identified as adhesive in all sheep leather threads. Collagen glue from other species (cattle, sheep, horse) was occasionally found in mixed adhesives. In two textiles, the finding of human proteins indicates past contamination due to handling or use. The analytical results show coherence between the fabrication patterns of animal-based metal threads and their probable geographical areas of manufacture, indicating that the study of materials and techniques provide further criteria to classify and group textiles, and trace correlations between manufacturing centers within Eurasian territories.

COL1A2 Barcoding: Bone Species Identification via Shotgun Proteomics

Species identification of fragmentary bones remains a challenging task in archeology and forensics. A species identification method for such fragmentary bones that has recently attracted interest is the use of bone collagen proteins. Here, we describe a method similar to DNA barcoding that reads collagen protein sequences in bone and automatically determines the species by performing sequence database searches. The method is almost identical to conventional shotgun proteomics analysis of bone samples, except that the database used by the SEQUEST search engine consisted only of entries for collagen type 1 alpha 2 (COL1A2) proteins from various vertebrates. Accordingly, the COL1A2 peptides that differ in sequence among species act as species marker peptides. In SEQUEST-based shotgun proteomics, the protein entries that contain more marker peptide sequences are assigned higher scores; therefore, the highest-scoring protein entry will be the COL1A2 entry for the species from which the analyzed bone was derived. We tested our method using bone samples from 30 vertebrate species and found that all species were correctly identified. In conclusion, COL1A2 can be used as a bone protein barcode and can be read through shotgun proteomics, allowing for automatic bone species identification. Data are available via ProteomeXchange with the identifier PXD045402.

Human and animal skin identified by palaeoproteomics in Scythian leather objects from Ukraine

Leather was one of the most important materials of nomadic Scythians, used for clothing, shoes, and quivers, amongst other objects. However, our knowledge regarding the specific animal species used in Scythian leather production remains limited. In this first systematic study, we used palaeoproteomics methods to analyse the species in 45 samples of leather and two fur objects recovered from 18 burials excavated at 14 different Scythian sites in southern Ukraine. Our results demonstrate that Scythians primarily used domesticated species such as sheep, goat, cattle, and horse for the production of leather, while the furs were made of wild animals such as fox, squirrel and feline species. The surprise discovery is the presence of two human skin samples, which for the first time provide direct evidence of the ancient Greek historian Herodotus' claim that Scythians used the skin of their dead enemies to manufacture leather trophy items, such as quiver covers. We argue that leather manufacture is not incompatible with a nomadic lifestyle and that Scythians possessed sophisticated leather production technologies that ensured stable supply of this essential material.

A simplified sample preparation for hair and skin proteins towards the application of archaeological fur and leather

Conventional protocols for proteomics analysis usually start by extracting or solubilizing the proteins from their substrates. This step can be challenging for archaeological proteins, when they are heavily contaminated or decayed. The remains of animal fur/leather objects from an early medieval burial in Trossingen (580 CE) from Southwest Germany were submitted to proteomics analysis for species identification. One leather sample (TS3) yielded enough proteins to be identified as cow using a urea-based extraction (method "U"), confirming the microscopic identification. But two other samples (TS1 and TS2), compacted in a greyish brittle matrix with embedded hair visible only under microscope, could not be characterized with that method. A series of tests was performed using reduction/alkylation with tris(2-carboxyethyl)phosphine/chloroacetamide at 95 °C directly on the matrix (method "95C"), with or without the use of paramagnetic beads as cleaning procedure (from the single-pot solid-phase-enhanced sample preparation or SP3). Hair keratins were best recovered in the fur samples when digestion was performed directly on the insoluble fraction after reduction/alkylation. For both samples TS1 and TS2, an ovicaprine species was identified, with TS1 firmly identified as sheep due to the exceptional preservation of keratins and keratin-associated proteins. The simplified protocol also showed improvements on the identification of collagen in the leather sample TS3. SIGNIFICANCE: North European burials had a strong tradition of bodies wrapped or covered in animal skins; textiles, furs, items of leather and other organic materials were essential parts of grave furnishings (as part of the deceased's clothing as well as grave goods) but are mostly only preserved as residues, uncharacterized layers or stains. Even well preserved finds like the waterlogged organic remains from Trossingen show strong limitations for visual identification. Because the traditional protocol was unable to extract proteins efficiently from the soil matrix in which the samples were embedded, a new method was devised that enabled the determination of the sampled fur remains as sheep and the leather fragments as cow leather. Analyses showed that the key step for accessing the proteins in the soiled archaeological samples was heating for 10 min at 95 °C with a solution of tris(2-carboxyethyl)phosphine/chloroacetamide (TCEP/CAA). The protocol proposed in this study offers to work on minute samples (1 mg of sample or less) and overcame the challenge of separating the proteins from their archaeological matrix. It offers interesting perspectives for archaeological sites or objects where clothing are suspected but hardly detectable, such as burial sites.

DNA and protein analyses of hair in forensic genetics

Hair is one of the most common pieces of biological evidence found at a crime scene and plays an essential role in forensic investigation. Hairs, especially non-follicular hairs, are usually found at various crime scenes, either by natural shedding or by forcible shedding. However, the genetic material in hairs is usually highly degraded, which makes forensic analysis difficult. As a result, the value of hair has not been fully exploited in forensic investigations and trials. In recent years, with advances in molecular biology, forensic analysis of hair has achieved remarkable strides and provided crucial clues in numerous cases. This article reviews recent developments in DNA and protein analysis of hair and attempts to provide a comprehensive solution to improve forensic hair analysis.

Paleoproteomics

Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.

Palaeoproteomics identifies beaver fur in Danish high-status Viking Age burials - direct evidence of fur trade

Fur is known from contemporary written sources to have been a key commodity in the Viking Age. Nevertheless, the fur trade has been notoriously difficult to study archaeologically as fur rarely survives in the archaeological record. In Denmark, fur finds are rare and fur in clothing has been limited to a few reports and not recorded systematically. We were therefore given access to fur from six Danish high status graves dated to the Viking Age. The fur was analysed by aDNA and palaeoproteomics methods to identify the species of origin in order to explore the Viking Age fur trade. Endogenous aDNA was not recovered, but fur proteins (keratins) were analysed by MALDI-TOF-MS and LC-MS/MS. We show that Viking Age skin clothing were often composites of several species, showing highly developed manufacturing and material knowledge. For example, fur was produced from wild animals while leather was made of domesticates. Several examples of beaver fur were identified, a species which is not native to Denmark, and therefore indicative of trade. We argue that beaver fur was a luxury commodity, limited to the elite and worn as an easily recognisable indicator of social status.

Are We Betting on the Wrong Horse? Insignificant Archaeological Leather Fragments Provide the First Evidence for the Exploitation of Horsehide in Renaissance Denmark

Large archaeological, organic materials can be difficult to preserve, conserve, and store in their entirety, which is why prioritisation is often necessary. Priority is generally given to recognisable objects rather than smaller fragments. Nevertheless, for archaeological leather, exactly such insignificant fragments can provide new information on the diversity of species exploited. In this pilot study, we use a Citizen Science approach for the first time to identify archaeological leather fragments using the protein-based method Zooarchaeology by Mass Spectrometry (ZooMS). By inviting the public to participate in archaeological research, the project’s first 52 samples, including both recognisable and unidentifiable objects, were analysed. We show that the participants not only generated good data, but also contributed to current knowledge by identifying two hitherto undescribed animal species for leather in medieval and Renaissance Copenhagen. The finding of deer suggests that Copenhagen citizens now and then had access to game through the nobility and the finding of horse suggests that the unclean status of horses was sometimes overlooked to exploit its hide. Our findings are promising for more identifications and the new knowledge the project will generate. The study calls into question how we prioritise and assign value to cultural heritage materials.

Leveraging palaeoproteomics to address conservation and restoration agendas

Archaeological and paleontological records offer tremendous yet often untapped potential for examining long-term biodiversity trends and the impact of climate change and human activity on ecosystems. Yet, zooarchaeological and fossil remains suffer various limitations, including that they are often highly fragmented and morphologically unidentifiable, preventing them from being optimally leveraged for addressing fundamental research questions in archaeology, paleontology, and conservation paleobiology. Here, we explore the potential of palaeoproteomics—the study of ancient proteins—to serve as a critical tool for creating richer, more informative datasets about biodiversity change that can be leveraged to generate more realistic, constructive, and effective conservation and restoration strategies into the future.

Trends in deamidation across archaeological bones, ceramics and dental calculus

The accumulation of post-translational modifications (PTMs) in proteins throughout the lifecycle has been studied for decades, particularly more so with the advent of soft-ionization mass spectrometry-based proteomic techniques. However, particular PTMs, such as the deamidations of asparagine and glutamine residues, continue to accumulate in proteins that remain into the forensic, archaeological, and palaeontological records. The accurate measurement of these ancient 'molecular timers' has been proposed as a method to not only differentiate between exogenous and endogenous proteins within complex mixtures (i.e., contamination), but also as a method of providing relative age estimations into geological time. In this study we explored the extent to which deamidation varies with chronological age across different proteins in bones, as well as investigated differences between proteins across dental calculus and archaeological ceramics. We also analysed the relationships between the observed extent of deamidation and the protein primary structure. We found that collagen obtained from archaeological bones showed a chronological dependence on the extent of deamidation observed, but only when they were from similar environments, supporting prior suggestions about 'thermal age' being a major influence on the deamidation observed. Our study on non-collagenous proteins (NCPs) in archaeological bones showed that while biglycan, and to a lesser extent chondroadherin, showed positive correlations between geological age and the extent of deamidation, others including fetuin-A and serum albumin did not. However, despite the well-known dependence of deamidation on the three-dimensional structure of the peptides, we were unable to find any clear correlation between the structural motifs of the peptides in archaeological bones and the extent of deamidation observed. Our analysis of a set of food proteins obtained from Neolithic archaeological ceramics in Çatalhöyük also showed similar deamidation levels irrespective of the protein structure. Overall, our results suggest that deamidation in archaeological samples could be useful for obtaining additional information beyond identification of species and tissue type, be that as a measure of protein endogeneity and potential contamination, or a measure of protein degradation, or as an indicator of thermal age and for relative dating; however, further research needs to be undertaken to understand why particular proteins are better for this than others, going beyond simple consideration of their secondary structure.

Forensic proteomics

Protein is a major component of all biological evidence, often the matrix that embeds other biomolecules such as polynucleotides, lipids, carbohydrates, and small molecules. The proteins in a sample reflect the transcriptional and translational program of the originating cell types. Because of this, proteins can be used to identify body fluids and tissues, as well as convey genetic information in the form of single amino acid polymorphisms, the result of non-synonymous SNPs. This review explores the application and potential of forensic proteomics. The historical role that protein analysis played in the development of forensic science is examined. This review details how innovations in proteomic mass spectrometry have addressed many of the historical limitations of forensic protein science, and how the application of forensic proteomics differs from proteomics in the life sciences. Two more developed applications of forensic proteomics are examined in detail: body fluid and tissue identification, and proteomic genotyping. The review then highlights developing areas of proteomics that have the potential to impact forensic science in the near future: fingermark analysis, species identification, peptide toxicology, proteomic sex estimation, and estimation of post-mortem intervals. Finally, the review highlights some of the newer innovations in proteomics that may drive further development of the field. In addition to potential impact, this review also attempts to evaluate the stage of each application in the development, validation and implementation process. This review is targeted at investigators who are interested in learning about proteomics in a forensic context and expanding the amount of information they can extract from biological evidence.

Real-time authentication of animal species origin of leather products using rapid evaporative ionization mass spectrometry and chemometric analysis

Increasing accounts of fraud and persistent labeling problems have brought the authenticity of leather products into question. In this study, we developed an extremely simplified workflow for real-time, in situ, and unambiguous authentication of leather samples using rapid evaporative ionization mass spectrometry (REIMS) coupled with an electric soldering iron. Initially, authentic leather samples from cattle, sheep, pig, deer, ostrich, crocodile, and snake were used to create a chemometric model based on principal component analysis and linear discriminant analysis algorithms. The validated multivariate statistical model was then used to analyze and generate live classifications of commercial leather samples. In addition to REIMS analysis, the microstructures of leathers were characterized by scanning electron microscopy to provide complementary information. The current study is expected to provide a high-throughput tool with superior efficiency and accuracy for authenticating the identity of leathers and other consumer products of biogenic origin.

Recent developments in using the molecular decay dating method: a review

The dating of organic findings is a fundamental task for many scientific fields. Radiocarbon dating is currently the most commonly used method. For wood, dendrochronology is another state‐of‐the‐art method. Both methods suffer from systematic restrictions, leading to samples that have not yet been able to be dated. Molecular changes over time are reported for many materials under different preservation conditions. Many of them are intrinsically monotonous. These monotonous molecular decay (MD) patterns can be understood as clocks that start at the time when a given molecule was formed. Factors that influence these clocks include input material composition and preservation conditions. Different wood species, degrees of pyrolysis, and pretreatments lead to different prediction models. Preservation conditions might change the speed of a given clock and lead to different prediction models. Currently published models for predicting the age of wood, paper, and parchment depend on infrared spectroscopy. In contrast to radiocarbon dating, dating via MD does not comprise a single methodology. Some clocks may deliver less precise results than the others. Ultimately, developing a completely different, new dating strategy‐such as MD dating–will help to bring to light a treasure trove of information hidden in the darkness of organic findings.

Ancient protein analysis in archaeology

The analysis of ancient proteins from paleontological, archeological, and historic materials is revealing insights into past subsistence practices, patterns of health and disease, evolution and phylogeny, and past environments. This review tracks the development of this field, discusses some of the major methodological strategies used, and synthesizes recent developments in archeological applications of ancient protein analysis. Moreover, this review highlights some of the challenges faced by the field and potential future directions, arguing that the development of minimally invasive or nondestructive techniques, strategies for protein authentication, and the integration of ancient protein analysis with other biomolecular techniques are important research strategies as this field grows.

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

Multi-omics can informally be described as the combined use of high-throughput techniques allowing the characterization of complete microbial communities by the sequencing/identification of total pools of biomolecules including DNA, proteins or metabolites. These techniques have allowed an unprecedented level of knowledge on complex microbial ecosystems, which is having key implications in land and marine ecology, industrial biotechnology or biomedicine. Multi-omics have recently been applied to artistic or archaeological objects, with the goal of either contributing to shedding light on the original context of the pieces and/or to inform conservation approaches. In this minireview, we discuss the application of -omic techniques to the study of prehistoric artworks and ancient man-made objects in three main technical blocks: metagenomics, proteomics and metabolomics. In particular, we will focus on how proteomics and metabolomics can provide paradigm-breaking results by unambiguously identifying peptides associated with a given, palaeo-cultural context; and we will discuss how metagenomics can be central for the identification of the microbial keyplayers on artworks surfaces, whose conservation can then be approached by a range of techniques, including using selected microorganisms as 'probiotics' because of their direct or indirect effect in the stabilization and preservation of valuable art objects.

Probabilistic Limit of Detection for Ricin Identification Using a Shotgun Proteomics Assay

Robust and highly specific methods for the detection of the protein toxin ricin are of interest to the law enforcement community. In previous studies, methods based on liquid chromatography-tandem mass spectrometry shotgun proteomics have been proposed. The successful implementation of this approach relies on specific data evaluation criteria addressing (1) the quality of the mass spectrometric data, (2) the confidence of peptide identifications (peptide-spectrum matches), and (3) the number and sequence specificity of peptides detected. We present such data evaluation criteria and use a novel approach to establish the limit of detection for this ricin assay. Specifically, we use logistic regression to determine the probability of detection for individual ricin peptides at different concentrations. We then apply basic rules from probability theory, combining these individual peptide probabilities into an overall assay limit of detection. This procedure yields an assay limit of detection for ricin at 42.5 ng on column or 21.25 ng/μL for a 2-μL injection. We also show that, despite the conventional wisdom that detergents are deleterious to mass spectrometric analyses, the presence of Tween-20 did not prevent detection of ricin peptides, and indeed assays performed in buffers that included Tween-20 gave better results than assays performed using other buffer formulations with or without detergent removal.

Palaeoproteomic identification of breast milk protein residues from the archaeological skeletal remains of a neonatal dog

Accurate postmortem estimation of breastfeeding status for archaeological or forensic neonatal remains is difficult. Confident identification of milk-specific proteins associated with these remains would provide direct evidence of breast milk consumption. We used liquid chromatography coupled to tandem mass spectrometry (MS) to confidently identify beta-lactoglobulin-1 (LGB1) and whey acidic protein (WAP), major whey proteins associated with a neonatal dog (Canis lupus familiaris) skeleton (430–960 cal AD), from an archaeological site in Hokkaido, Japan. The age at death of the individual was estimated to be approximately two weeks after birth. Protein residues extracted from rib and vertebra fragments were analyzed and identified by matching tandem MS spectra against the dog reference proteome. A total of 200 dog protein groups were detected and at least one peptide from canine LGB1 and two peptides from canine WAP were confidently identified. These milk proteins most probably originated from the mother’s breast milk, ingested by the neonate just before it died. We suggest the milk diffused outside the digestive apparatus during decomposition, and, by being absorbed into the bones, it partially preserved. The result of this study suggests that proteomic analysis can be used for postmortem reconstruction of the breastfeeding status at the time of death of neonatal mammalian, by analyzing their skeletal archaeological remains. This method is also applicable to forensic and wildlife studies.

Species identification of Bombyx mori and Antheraea pernyi silk via immunology and proteomics

In recent years, increasing attention has been paid to the origin, transmission and communication of silk. However, this is still an unsolved mystery in archaeology. The identification of silk-producing species, especially silk produced by Bombyx mori (B. mori) and Antheraea pernyi (A. pernyi), is of key significance to address this challenge. In this study, two innovative methods, i.e. immunology and proteomics, were proposed and successfully established for the species identification of silks. ELISAs result demonstrated that the two prepared antibodies exhibited high sensitivity and specificity in distinguishing B. mori and A. pernyi silk. No cross-reactivity with each other was observed. Moreover, biomarkers were obtained for Bombyx and Antheraea through proteomic analysis. It was also confirmed that the biomarkers were suitable for identifying the species that produced a given silk sample. Compared with conventional methods for distinguishing silk species, immunological and proteomics techniques used in tandem can provide intact information and have the potential to provide accurate and reliable information for species identification.

Characterization of proteins in cultural heritage using MALDI–TOF and LC–MS/MS mass spectrometric techniques

Identification of proteinaceous materials in artworks is of high interest to restorers-conservators, art historians and archaeologists, because it helps to shed light on the used painting techniques, to attribute unknown artworks, to make conclusions on prehistoric diets, etc. The chapter is devoted to the mass spectrometry instrumentation, evaluation of obtained data and it is showing several examples of the application of matrix-assisted laser desorption/ionization–time-of-flight and liquid chromatography–electrospray ionization–quadrupole–time-of-flight mass spectrometers on cultural heritage samples.

Semi-Nondestructive Certification of Crocodilian Leather by LC-MS Detection of Collagen Marker Peptides

Leather produced from crocodile, alligator, and caiman skin is widely used in the fashion industry. Crocodilian leather is generally more expensive than mammalian leather, and the value greatly differs even between the crocodilian species. However, inappropriate labeling of the animal source on leather products sometimes arises from accidental or fraudulent substitution, which is difficult to unambiguously detect by existing methods. In the present study, animal source identification of crocodilian leather was carried out using type I collagen-derived marker peptides generated after dechroming, heat denaturation, and trypsin digestion. Definitive discrimination between the three crocodilian species and also a related species, lizard, was achieved based on the detection patterns of selected six marker peptides, determined by LC-MS. Furthermore, powdering of the leather samples enabled a reduction in the sample amount required and allowed the elimination of the dechroming step. Approximately 100 μg of powder was taken from commercial leather watch straps by filing, resulting in only slight damage to the undersides of the straps. The animal sources of the crocodilian products and also a crocodile-embossed calf product were successfully identified using a combination of the crocodilian marker peptides and previously established mammalian marker peptides. This semi-nondestructive species identification method is not only useful for certification of leather products but also for monitoring of international trade of leather and skin.

A guide to ancient protein studies

Palaeoproteomics is an emerging neologism used to describe the application of mass spectrometry-based approaches to the study of ancient proteomes. As with palaeogenomics (the study of ancient DNA), it intersects evolutionary biology, archaeology and anthropology, with applications ranging from the phylogenetic reconstruction of extinct species to the investigation of past human diets and ancient diseases. However, there is no explicit consensus at present regarding standards for data reporting, data validation measures or the use of suitable contamination controls in ancient protein studies. Additionally, in contrast to the ancient DNA community, no consolidated guidelines have been proposed by which researchers, reviewers and editors can evaluate palaeoproteomics data, in part due to the novelty of the field. Here we present a series of precautions and standards for ancient protein research that can be implemented at each stage of analysis, from sample selection to data interpretation. These guidelines are not intended to impose a narrow or rigid list of authentication criteria, but rather to support good practices in the field and to ensure the generation of robust, reproducible results. As the field grows and methodologies change, so too will best practices. It is therefore essential that researchers continue to provide necessary details on how data were generated and authenticated so that the results can be independently and effectively evaluated. We hope that these proposed standards of practice will help to provide a firm foundation for the establishment of palaeoproteomics as a viable and powerful tool for archaeologists, anthropologists and evolutionary biologists.

Follow-up on the characterization of peptidic markers in hair and fur for the identification of common North American species

RATIONALE

Species identification of hair is routinely done by microscopic analysis. Following previous studies that used protein analysis to characterize species markers in hair and wool, the present work aims at covering a larger number of species and to ultimately offer a method for rapid hair identification in forensics and archaeology.

METHODS

Hair is mostly made of alpha-keratins; these proteins have only been sequenced in a handful of species and most animal families are under-represented. Using a methodology developed for the characterization of peptidic markers in tissues such as bone (peptide mass fingerprinting or PMF) and commonly applied on collagen, hair from common North American fur-bearing species was analyzed by MALDI-TOF-MS to obtain peptidic profiles.

RESULTS

Alpha-keratin peptides that are typically dominant on peptide mass profiles of hair were chosen as markers. Matching peaks were identified for each species tested and compared to known sequences from related organisms whenever possible. The markers were used to create a flowchart to narrow down identification to the family level.

CONCLUSIONS

The methodology was developed on a limited numbers of markers chosen for their variability and reliability on the peptide mass fingerprint. In the absence of genetic sequences, this strategy is a quick way to compare species from a common geographic origin. The work presented here was focused on North American species but could be applied to other animal families.

Molecular markers in keratins from Mysticeti whales for species identification of baleen in museum and archaeological collections

Baleen has been harvested by indigenous people for thousands of years, as well as collected by whalers as an additional product of commercial whaling in modern times. Baleen refers to the food-filtering system of Mysticeti whales; a full baleen rack consists of dozens of plates of a tough and flexible keratinous material that terminate in bristles. Due to its properties, baleen was a valuable raw material used in a wide range of artefacts, from implements to clothing. Baleen is not widely used today, however, analyses of this biomolecular tissue have the potential to contribute to conservation efforts, studies of genetic diversity and a better understanding of the exploitation and use of Mysticeti whales in past and recent times. Fortunately, baleen is present in abundance in museum natural history collections. However, it is often difficult or impossible to make a species identification of manufactured or old baleen. Here, we propose a new tool for biomolecular identification of baleen based on its main structural component alpha-keratin (the same protein that makes up hair and fingernails). With the exception of minke whales, alpha-keratin sequences are not yet known for baleen whales. We therefore used peptide mass fingerprinting to determine peptidic profiles in well documented baleen and evaluated the possibility of using this technique to differentiate species in baleen samples that are not adequately identified or are unidentified. We examined baleen from ten different species of whales and determined molecular markers for each species, including species-specific markers. In the case of the Bryde's whales, differences between specimens suggest distinct species or sub-species, consistent with the complex phylogeny of the species. Finally, the methodology was applied to 29 fragments of baleen excavated from archaeological sites in Labrador, Canada (representing 1500 years of whale use by prehistoric people), demonstrating a dominance of bowhead whale (Balaena mysticetus) in the archaeological assemblage and the successful application of the peptide mass fingerprinting technique to identify the species of whale in unidentified and partially degraded samples.

Preservation of the metaproteome: variability of protein preservation in ancient dental calculus

Proteomic analysis of dental calculus is emerging as a powerful tool for disease and dietary characterisation of archaeological populations. To better understand the variability in protein results from dental calculus, we analysed 21 samples from three Roman-period populations to compare: 1) the quantity of extracted protein; 2) the number of mass spectral queries; and 3) the number of peptide spectral matches and protein identifications. We found little correlation between the quantity of calculus analysed and total protein identifications, as well as no systematic trends between site location and protein preservation. We identified a wide range of individual variability, which may be associated with the mechanisms of calculus formation and/or post-depositional contamination, in addition to taphonomic factors. Our results suggest dental calculus is indeed a stable, long-term reservoir of proteins as previously reported, but further systematic studies are needed to identify mechanisms associated with protein entrapment and survival in dental calculus.

Proteomic profiling of archaeological human bone

Ancient protein analysis provides clues to human life and diseases from ancient times. Here, we performed shotgun proteomics of human archeological bones for the first time, using rib bones from the Hitotsubashi site (AD 1657-1683) in Tokyo, called Edo in ancient times. The output data obtained were analysed using Gene Ontology and label-free quantification. We detected leucocyte-derived proteins, possibly originating from the bone marrow of the rib. Particularly prevalent and relatively high expression of eosinophil peroxidase suggests the influence of infectious diseases. This scenario is plausible, considering the overcrowding and unhygienic living conditions of the Edo city described in the historical literature. We also observed age-dependent differences in proteome profiles, particularly for proteins involved in developmental processes. Among them, alpha-2-HS-glycoprotein demonstrated a strong negative correlation with age. These results suggest that analysis of ancient proteins could provide a useful indicator of stress, disease, starvation, obesity and other kinds of physiological and pathological information.

A whole mitochondria analysis of the Tyrolean Iceman's leather provides insights into the animal sources of Copper Age clothing

The attire of the Tyrolean Iceman, a 5,300-year-old natural mummy from the Ötzal Italian Alps, provides a surviving example of ancient manufacturing technologies. Research into his garments has however, been limited by ambiguity surrounding their source species. Here we present a targeted enrichment and sequencing of full mitochondrial genomes sampled from his clothes and quiver, which elucidates the species of production for nine fragments. Results indicate that the majority of the samples originate from domestic ungulate species (cattle, sheep and goat), whose recovered haplogroups are now at high frequency in today’s domestic populations. Intriguingly, the hat and quiver samples were produced from wild species, brown bear and roe deer respectively. Combined, these results suggest that Copper Age populations made considered choices of clothing material from both the wild and domestic populations available to them. Moreover, these results show the potential for the recovery of complete mitochondrial genomes from degraded prehistoric artefacts.

A Rapid and Simple LC-MS Method Using Collagen Marker Peptides for Identification of the Animal Source of Leather

Identification of the animal source of leather is difficult using traditional methods, including microscopic observation and PCR. In the present study, a LC-MS method was developed for detecting interspecies differences in the amino acid sequence of type I collagen, which is a major component of leather, among six animals (cattle, horse, pig, sheep, goat, and deer). After a dechroming procedure and trypsin digestion, six tryptic peptides of type I collagen were monitored by LC-MS in multiple reaction monitoring mode for the animal source identification using the patterns of the presence or absence of the marker peptides. We analyzed commercial leathers from various production areas using this method, and found some leathers in which the commercial label disagreed with the identified animal source. Our method enabled rapid and simple leather certification and could be applied to other animals whether or not their collagen sequences are available in public databases.

Rapid and Accurate Identification of Animal Species in Natural Leather Goods by Liquid Chromatography/Mass Spectrometry

The demand for leather goods has grown globally in recent years. Industry revenue is forecast to reach $91.2 billion by 2018. There is an ongoing labelling problem in the leather items market, in that it is currently impossible to identify the species that a given piece of leather is derived from. To address this issue, we developed a rapid and simple method for the specific identification of leather derived from cattle, horses, pigs, sheep, goats, and deer by analysing peptides produced by the trypsin-digestion of proteins contained in leather goods using liquid chromatography/mass spectrometry. We determined species-specific amino acid sequences by liquid chromatography/tandem mass spectrometry analysis using the Mascot software program and demonstrated that collagen α-1(I), collagen α-2(I), and collagen α-1(III) from the dermal layer of the skin are particularly useful in species identification.

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

Tissue-thin parchment made it possible to produce the first pocket Bibles: Thousands were made in the 13th century. The source of this parchment, often called "uterine vellum," has been a long-standing controversy in codicology. Use of the Latin term abortivum in many sources has led some scholars to suggest that the skin of fetal calves or sheep was used. Others have argued that it would not be possible to sustain herds if so many pocket Bibles were produced from fetal skins, arguing instead for unexpected alternatives, such as rabbit. Here, we report a simple and objective technique using standard conservation treatments to identify the animal origin of parchment. The noninvasive method is a variant on zooarchaeology by mass spectrometry (ZooMS) peptide mass fingerprinting but extracts protein from the parchment surface by using an electrostatic charge generated by gentle rubbing of a PVC eraser on the membrane surface. Using this method, we analyzed 72 pocket Bibles originating in France, England, and Italy and 293 additional parchment samples that bracket this period. We found no evidence for the use of unexpected animals; however, we did identify the use of more than one mammal species in a single manuscript, consistent with the local availability of hides. These results suggest that ultrafine vellum does not necessarily derive from the use of abortive or newborn animals with ultrathin hides, but could equally well reflect a production process that allowed the skins of maturing animals of several species to be rendered into vellum of equal quality and fineness.