Deamidation at asparagine and glutamine as a major modification upon deterioration/aging of proteinaceous binders in mural paintings

Molecular Characterization of Adhesives (Glue Lining Pastes) Used in Restoration

The molecular characterization of samples from works of art can provide valuable insights into the composition of ancient restoration materials and their conservation state. Here, we present a novel analytical protocol for the molecular characterization of a specific adhesive used in historical painting restoration, known as "glue lining pastes." Due to the high molecular complexity of these adhesives, we propose a multistep extraction protocol to recover and fractionate from a single microsample the three main classes of biomolecules contained in glue pastes (lipids, polysaccharides, and proteins). High-performance separation coupled with high-resolution mass spectrometry (MS) techniques were applied to the isolated fractions to identify specific components. The proposed method was optimized using test specimens of various traditional glue pastes applied to canvases and successfully applied to a historical glue paste sample from the 17th-century painting "La fuga in Egitto," part of the Pagliara collection at the University Suor Orsola Benincasa (Naples, Italy). The data collected in this work provide insights into the specific recipe used for adhesive preparation, supporting artistic and historical interpretations and contributing to a broader understanding of old restoration practices. Data are available via ProteomeXchange with the identifier PXD051480.

Low-Invasive Sampling Method with Tape-Disc Sampling for the Taxonomic Identification of Archeological and Paleontological Bones by Proteomics

Collagen from paleontological bones is an important organic material for isotopic measurement, radiocarbon analysis, and paleoproteomic analysis to provide information on diet, dating, taxonomy, and phylogeny. Current paleoproteomic methods are destructive and require from a few milligrams to several tens of milligrams of bone for analysis. In many cultures, bones are raw materials for artifacts that are conserved in museums, which hampers damage to these precious objects during sampling. Here, we describe a low-invasive sampling method that identifies collagen, taxonomy, and post-translational modifications from Holocene and Upper Pleistocene bones dated to 130,000 and 150 BC using dermatological skin tape discs for sampling. The sampled bone micropowders were digested following our highly optimized enhanced filter-aided sample preparation protocol and then analyzed by MALDI FTICR MS and LC-MS/MS for identifying the genus taxa of the bones. We show that this low-invasive sampling does not deteriorate the bones and achieves results similar to those obtained by more destructive sampling. Moreover, this sampling method can be carried out at archeological sites or in museums.

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.

Artefact Profiling: Panomics Approaches for Understanding the Materiality of Written Artefacts

This review explains the strategies behind genomics, proteomics, metabolomics, metallomics and isotopolomics approaches and their applicability to written artefacts. The respective sub-chapters give an insight into the analytical procedure and the conclusions drawn from such analyses. A distinction is made between information that can be obtained from the materials used in the respective manuscript and meta-information that cannot be obtained from the manuscript itself, but from residues of organisms such as bacteria or the authors and readers. In addition, various sampling techniques are discussed in particular, which pose a special challenge in manuscripts. The focus is on high-resolution, non-targeted strategies that can be used to extract the maximum amount of information about ancient objects. The combination of the various omics disciplines (panomics) especially offers potential added value in terms of the best possible interpretations of the data received. The information obtained can be used to understand the production of ancient artefacts, to gain impressions of former living conditions, to prove their authenticity, to assess whether there is a toxic hazard in handling the manuscripts, and to be able to determine appropriate measures for their conservation and restoration.

Review of recent advances on the use of mass spectrometry techniques for the study of organic materials in painted artworks

The study of painted artworks using scientific methods is fundamental for understanding the techniques used in their creation and their appropriate conservation. The ethical constraints involved in the handling of, and sampling from, these objects has steered recent developments in the field of Heritage science towards a range of new non-invasive/non-destructive spectroscopic techniques capable of providing important insights into their elemental or bulk chemical compositions. Due to the inherent complexities of heritage artefacts, however, their organic components are especially difficult to study in this way and their identification and degradation pathways are thus often best investigated using mass spectrometric (MS) techniques. The versatility, sensitivity and specificity of MS techniques are constantly increasing, with technological advances pushing the boundaries of their use in this field. The progress in the past ten years in the use of MS techniques for the analysis of paint media are described in the present review. While some historical context is included, the body of the review is structured around the five most widely used or emerging capabilities offered by MS. The first pertains to the use of spatially resolved MS to obtain chemical maps of components in cross-sections, which may yield information on both inorganic and organic materials, while the second area describes the development of novel sample preparation approaches for gas chromatography (GC)-MS to allow simultaneous analysis of a variety of components. The third focuses on thermally assisted analysis (either with direct MS or coupled with GC-MS), a powerful tool for studying macromolecules requiring zero (or minimal) sample pre-treatment. Subsequently, the use of soft ionisation techniques often combined with high-resolution MS for the study of peptides (proteomics) and other macromolecules (such as oligosaccharides and triglycerides) is outlined. The fifth area covers the advances in radiocarbon dating of painting components with accelerator MS (AMS). Lastly, future applications of other MS techniques to the study of paintings are mentioned; such as direct analysis in real time MS (DART-MS) and stable isotope ratio MS (IRMS). The latter, having proven its efficiency for the study of lipids in archaeological artefacts, is envisioned to become a valuable tool for this area, whereas DART-MS is already being utilised to study the surface composition of various museum objects. Rapid technological advances, resulting in increased sensitivity and selectivity of MS techniques, are opening up new approaches for paintings analysis, overcoming the fundamental hurdle of sample size available for destructive analysis. Importantly, while the last decade has seen proteomics applications come to the fore, this review aims to emphasise the wider potential of advanced MS techniques for the study of painting materials and their conservation.

Visible Light Induces Site-Specific Oxidative Heavy Chain Fragmentation of a Monoclonal Antibody (IgG1) Mediated by an Iron(III)-Containing Histidine Buffer

Fragmentation of therapeutic monoclonal antibodies represents a critical quality attribute. Here, we report a novel visible light-induced heavy chain fragmentation of IgG1 mediated by an Fe(III)-containing histidine (His) buffer. Based on non-reducing sodium dodecylsulfate-polyacrylamide gel electrophoresis and mass spectrometry analysis, IgG1 fragments with apparent molecular weights of ∼130, ∼110, and ∼22 kDa were detected in photo-irradiated samples and were mechanistically rationalized with an oxidative cleavage at Thr²⁵⁹. Specifically, the reactions are proposed to involve the generation of an intermediary alkoxyl radical, which undergoes β-cleavage to yield a glycyl radical. The latter either converts into Gly or adds oxygen and follows a peroxyl radical chemistry. The cleavage process requires the presence of His, while only negligible yields of cleavage products are formed when His is replaced by acetate, succinate, or phosphate buffer. Importantly, the fragmentation can be prevented by ethylenediaminetetraacetic acid (EDTA) only when the EDTA concentrations are in significant excess over the concentrations of Fe(III) and proteins, suggesting a strong binding between Fe(III) and IgG1.

Palaeoproteomics guidelines to identify proteinaceous binders in artworks following the study of a 15th-century painting by Sandro Botticelli's workshop

Undertaking the conservation of artworks informed by the results of molecular analyses has gained growing importance over the last decades, and today it can take advantage of state-of-the-art analytical techniques, such as mass spectrometry-based proteomics. Protein-based binders are among the most common organic materials used in artworks, having been used in their production for centuries. However, the applications of proteomics to these materials are still limited. In this work, a palaeoproteomic workflow was successfully tested on paint reconstructions, and subsequently applied to micro-samples from a 15th-century panel painting, attributed to the workshop of Sandro Botticelli. This method allowed the confident identification of the protein-based binders and their biological origin, as well as the discrimination of the binder used in the ground and paint layers of the painting. These results show that the approach is accurate, highly sensitive, and broadly applicable in the cultural heritage field, due to the limited amount of starting material required. Accordingly, a set of guidelines are suggested, covering the main steps of the data analysis and interpretation of protein sequencing results, optimised for artworks.

Palmyrene Polychromy: Investigations of Funerary Portraits from Palmyra in the Collections of the Ny Carlsberg Glyptotek, Copenhagen

The current study is the first comprehensive investigation of the polychromy of Palmyrene funerary portraits. It presents the technical examinations of six portraits (ca. 150–250 CE) from the collection of the Ny Carlsberg Glyptotek, illustrating the marvellous splendour of the cultural heritage of ancient Palmyra. The six portraits were examined with various analytical methods, including microscopy, ultraviolet-induced visible fluorescence imaging and visible light-induced infrared luminescence imaging, X-ray fluorescence spectroscopy, scanning electron microscopy coupled to energy-dispersive X-ray spectroscopy, and Fourier transform infrared spectroscopy. Finally, two samples were collected for liquid chromatography–tandem mass spectrometry to obtain the amino acid sequence information. Various pigments were detected in the polychromy including lapis lazuli, pyromorphite, mimetite, yellow ochre, red ochre, a red lake, lead carbonate, zinc oxide, bone black, and charcoal black. The proteinaceous binding medium was identified as collagen-based and possibly also keratin-based animal glue. The examinations of the Palmyrene portraits in the Ny Carlsberg Glyptotek have proven that these artefacts, despite their current uniform, white appearance, originally presented themselves in a wealth of colours. This is illustrated by the digital reconstructions carried out of two of the examined portraits, which show how the original painting of these portraits would have given them an entirely different expression from what we see today.

Mass spectrometry in art conservation-With focus on paintings

Conservation of historic artifacts has been a multidisciplinary field from its very beginning. Traditionally, it has been and still is associated with the history of art. It applies knowledge from technical and basic sciences, adapting their solutions to its goals. At present, however, a new tendency is clearly emerging-scientific research is starting to play an increasingly important role not only as a service, but also by proposing new solutions both in the traditional conservation areas and in new areas of conservation activities. The above trend opens up new perspectives for the field of preservation of our heritage but may also create new threats. Therefore, the conservators' caution in introducing new technologies should always be justified; after all, they are responsible for the effects of any activities on the historic objects. This, quite selective review, discusses application of mass spectrometry techniques for the detection of various components that are important to the conservators of our heritage with particular focus on paintings. The text also contains some basic knowledge of technical details to introduce the methodology to a broader group of professionals.

Introducing protein deamidation: Landmark discoveries, societal outreach, and tentative priming workflow to address deamidation

Our current knowledge on protein deamidation results from a journey that started almost 100 years ago, when a handful of researchers first described the non-enzymatic "desamidation" of glutamine, and the effect of different anions on the catalytic rate of the reaction. Since then, the field has tremendously expended and now finds outreach in very diverse areas. In light of all the recent articles published in these areas, it seemed timely to propose an integrated review on the subject, including a short historical overview of the landmark discoveries in the field, highlighting the current global positioning of protein deamidation in biology and non-biology fields, and concluding with a workflow for those asking if a protein can deamidate, and identify the residues involved. This review is essentially intended to provide newcomers in the field with an overview of how deamidation has penetrated our society and what tools are currently at hand to identify and quantify protein deamidation.

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

The origins, prevalence and nature of dairying have been long debated by archaeologists. Within the last decade, new advances in high-resolution mass spectrometry have allowed for the direct detection of milk proteins from archaeological remains, including ceramic residues, dental calculus, and preserved dairy products. Proteins recovered from archaeological remains are susceptible to post-excavation and laboratory contamination, a particular concern for ancient dairying studies as milk proteins such as beta-lactoglobulin (BLG) and caseins are potential laboratory contaminants. Here, we examine how site-specific rates of deamidation (i.e., deamidation occurring in specific positions in the protein chain) can be used to elucidate patterns of peptide degradation, and authenticate ancient milk proteins. First, we characterize site-specific deamidation patterns in modern milk products and experimental samples, confirming that deamidation occurs primarily at low half-time sites. We then compare this to previously published palaeoproteomic data from six studies reporting ancient milk peptides. We confirm that site-specific deamidation rates, on average, are more advanced in BLG  recovered from ancient dental calculus and pottery residues. Nevertheless, deamidation rates displayed a high degree of variability, making it challenging to authenticate samples with relatively few milk peptides. We demonstrate that site-specific deamidation is a useful tool for identifying modern contamination but highlight the need for multiple lines of evidence to authenticate ancient protein data.

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

We used palaeoproteomics and peptide mass fingerprinting to obtain secure species identifications of key specimens of early domesticated fauna from South Africa, dating to ca. 2000 BP. It can be difficult to distinguish fragmentary remains of early domesticates (sheep) from similar-sized local wild bovids (grey duiker, grey rhebok, springbok-southern Africa lacks wild sheep) based on morphology alone. Our analysis revealed a Zooarchaeology by Mass Spectrometry (ZooMS) marker (m/z 1532) present in wild bovids and we demonstrate through LC-MS/MS that it is capable of discriminating between wild bovids and caprine domesticates. We confirm that the Spoegrivier specimen dated to 2105 ± 65 BP is indeed a sheep. This is the earliest directly dated evidence of domesticated animals in southern Africa. As well as the traditional method of analysing bone fragments, we show the utility of minimally destructive sampling methods such as PVC eraser and polishing films for successful ZooMS identification. We also show that collagen extracted more than 25 years ago for the purpose of radiocarbon dating can yield successful ZooMS identification. Our study demonstrates the importance of developing appropriate regional frameworks of comparison for future research using ZooMS as a method of biomolecular species identification.

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

Identification and characterization of ancient proteins still require technical developments towards non-invasiveness, sensitivity, versatility and ease of use of the analyses. We report that the enzyme functionalized films, described in Cicatiello et al. (2018), can be used efficiently on the surface of different objects ranging from fixative-coated paper to canvas to the coating on an albumen photograph, as well as the much harder surfaces of ivory objects and the proteinaceous binders in the decoration of a wooden Egyptian coffin. The mixture of digested peptides that are efficiently captured on the functionalized surface are also amenable to LC-MS/MS analysis, which is necessary to confidently identify chemical modifications induced upon degradation, in order to characterize the conservation state of proteins. Moreover, in a two-step procedure, we have combined the trypsin functionalized film with a PNGaseF functionalized film, which adds a deglycosylation pretreatment allowing improved detection of glycosylated proteins. SIGNIFICANCE: User friendly trypsin functionalized films were implemented to expand their potential as versatile, modular tools that can be widely exploited in the world of diagnosis of cultural heritage objects, ancient proteins, and palaeoproteomics: a procedure that could be carried out by conservators or archaeologists first on-site and later analysed with standard MS techniques.

Ionisation bias undermines the use of matrix-assisted laser desorption/ionisation for estimating peptide deamidation: Synthetic peptide studies demonstrate electrospray ionisation gives more reliable response ratios

RATIONALE

Although mass spectrometry (MS) is routinely used to determine deamination in peptide mixtures, the effects of the choice of ionisation source have not yet been investigated. In particular, matrix-assisted laser desorption/ionisation (MALDI) has become a popular tool with which to measure levels of glutamine deamidation in ancient proteins. Here we use model synthetic peptides to rigorously compare MALDI and electrospray ionisation (ESI).

METHODS

We used two synthetic peptides, with glutamine (Q) in one substituted for glutamic acid (E) in the other, to investigate the suitability of MALDI and ESI sources for the assessment of deamidation in peptides using MS. We also compared measurements of the same Q- and E-containing peptide mixtures using two different mass analysers (time-of-flight (TOF) and Fourier transform ion cyclotron resonance (FT-ICR)).

RESULTS

When standard mixtures of the Q- and E-containing peptides were analysed using MALDI, under-representation of the E-containing peptide was observed. This observation was consistent between analyses carried out using either TOF or FT-ICR-MS. When the same mixtures were analysed using ESI FT-ICR-MS, no ionisation bias was observed.

CONCLUSIONS

MALDI may not be a suitable ionisation method for the determination of deamidation in peptide mixtures. However, ESI was successfully used to determine the ratio in known mixtures of Q- and E-containing peptides. These preliminary observations warrant further investigation into ionisation bias when measuring deamidation in other peptide sequences.

Fine Endmesolithic fish caviar meal discovered by proteomics in foodcrusts from archaeological site Friesack 4 (Brandenburg, Germany)

The role of aquatic resources in ancient economies and paleodiet is important for understanding the evolution of prehistorical societies. Charred food remains from ancient pottery are valuable molecular evidence of dietary habits in antiquity. However, conventional archaeometric approaches applied in their analysis lack organismal specificity, are affected by abundant environmental contaminants, do not elucidate food processing recipes and are limited in the inland regions where diverse dietary resources are available. We performed proteomics analysis of charred organic deposits adhered on early ceramics from Mesolithic-Neolithic inland site Friesack 4 (Brandenburg, Germany). One of pots—a small coarse bowl radiocarbon dated to the end of the 5^th millennium BC—was attributed to Endmesolithic pottery. Proteomics of foodcrust from this vessel identified fine carp roe meal and revealed details of a prehistorical culinary recipe. Ancient proteins were unequivocally distinguished from contemporary contaminants by computing deamidation ratios of glutamine residues. These data paint a broader picture of the site-specific exploitation of aquatic resources and contribute to better understanding of the dietary context of Neolithic transition in European inland.

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

Ahead of display, a non-original layer was observed on the surface of a fragment of a wall painting by Ambrogio Lorenzetti (active 1319, died 1348/9). FTIR analysis suggested proteinaceous content. Mass spectrometry was used to better characterise this layer and revealed two protein components: sheep and cow glue and chicken and duck egg white. Analysis of post-translational modifications detected several photo-oxidation products, which suggest that the egg experienced prolonged exposure to UV light and was likely applied long before the glue layer. Additionally, glycation products detected may indicate naturally occurring glycoprotein degradation or reaction with a carbohydrate material such as starch, identified by ATR-FTIR in a cross-section of a sample taken from the painting. Palaeoproteomics is shown to provide detailed characterisation of organic layers associated with mural paintings and therefore aids reconstruction of the conservation history of these objects.

Exploring Biological and Geological Age-related Changes through Variations in Intra- and Intertooth Proteomes of Ancient Dentine

Proteomic analyses are becoming more widely used in archeology not only due to the greater preservation of proteins in ancient specimens than DNA but also because they can offer different information, particularly relating to compositional preservation and potentially a means to estimate biological and geological age. However, it remains unclear to what extent different burial environments impact these aspects of proteome decay. Teeth have to date been much less studied than bone but are ideal to explore how proteins decay with time due to the negligible turnover that occurs in dentine relative to bone. We investigated the proteome variability and deamidation levels of different sections of molar teeth from archeological bovine mandibles as well as their mandibular bone. We obtained a greater yield of proteins from the crown of the teeth but did not find differences between the different molars analyzed within each mandible. We also obtained the best variety of protein from a well-preserved mandible that was not the youngest one in terms of chronological age, showing the influence of the preservation conditions on the final proteomic outcome. Intriguingly, we also noticed an increase in abundance levels of fetuin-A in biologically younger mandibles as reported previously, but the opposite trend in tooth dentine. Interestingly, we observed higher glutamine deamidation levels in teeth from the geologically oldest mandible despite it being the biologically youngest specimen, showing that the archeological age strongly impacts on the level of deamidations observed, much more so than biological aging. This indicates that the glutamine deamidation ratio of selected peptides may act as a good predictor of the relative geochronological age of archeological specimens.

Forensic proteomics for the evaluation of the post-mortem decay in bones

Current methods for evaluation the of post-mortem interval (PMI) of skeletal remains suffer from poor accuracy due to the great number of variables that affect the diagenetic process and to the lack of specific guidelines to address this issue. During decomposition, proteins can undergo cumulative decay over the time, resulting in a decrease in the range and abundance of proteins present (i.e., the proteome) in different tissues as well as in an increase of post-translational modifications occurring in these proteins. In this study, we investigate the applicability of bone proteomic analyses to simulated forensic contexts, looking for specific biomarkers that may help the estimation of PMI, as well as evaluate a previously discovered marker for the estimation of biological age. We noticed a reduction of particular plasma and muscle proteins with increasing PMIs, as well as an increased deamidation of biglycan, a protein with a role in modulating bone growth and mineralization. We also corroborated our previous results regarding the use of fetuin-A as a potential biomarker for the estimation of age-at-death, demonstrating the applicability and the great potential that proteomics may have towards forensic sciences.

SIGNIFICANCE

The estimation of the post-mortem interval has a key role in forensic investigations, however nowadays it still suffers from poor reliability, especially when body tissues are heavily decomposed. Here we propose for the first time the application of bone proteomics to the estimation of the time elapsed since death and found several new potential biomarkers to address this, demonstrating the applicability of proteomic analyses to forensic sciences.

LERLIC-MS/MS for In-depth Characterization and Quantification of Glutamine and Asparagine Deamidation in Shotgun Proteomics

Characterization of protein deamidation is imperative to decipher the role(s) and potentialities of this protein posttranslational modification (PTM) in human pathology and other biochemical contexts. In order to perform characterization of protein deamidation, we have recently developed a novel long-length electrostatic repulsion-hydrophilic interaction chromatography-tandem mass spectrometry (LERLIC-MS/MS) method which can separate the glutamine (Gln) and asparagine (Asn) isoform products of deamidation from model compounds to highly complex biological samples. LERLIC-MS/MS is, therefore, the first shotgun proteomics strategy for the separation and quantification of Gln deamidation isoforms. We also demonstrate, as a novelty, that the sample processing protocol outlined here stabilizes the succinimide intermediate allowing its characterization by LERLIC-MS/MS. Application of LERLIC-MS/MS as shown in this video article can help to elucidate the currently unknown molecular arrays of protein deamidation. Additionally, LERLIC-MS/MS provides further understanding of the enzymatic reactions that encompass deamidation in distinct biological backgrounds.

GC/MS and proteomics to unravel the painting history of the lost Giant Buddhas of Bāmiyān (Afghanistan)

A chemical investigation of the organic paint binders of the Giant Buddhas of Bāmiyān was performed using an analytical approach based on mass spectrometry, combining traditional gas chromatography/mass spectrometry protocols with advanced proteomics methodologies. The research was carried out on a selection of rescued fragments. The data revealed the use of egg proteins as the paint binders of the original layers, in accordance with the traditional use of this proteinaceous medium in antiquity, spanning from the Mediterranean basin to the Far East, and already in the Bronze Age. Egg tempera was thus known to artists of the region in the first centuries AD, probably also due to the position of the Bāmiyān valley, which was connected to the Silk Road. Milk was found in the first historical overpaintings. A new proteomics approach was used, which was able to identify the source of the milk proteins present in the restoration layers, despite their age and degradation. In particular cow’s and goat's milk were both found, in agreement with the documented presence of rich pastures in the Bāmiyān valley when the historical restorations were carried out. Investigating the materials of the Giant Buddhas not only enabled us to obtain isolated data on these invaluable works of art, which are now lost, but contributes to understanding the big “puzzle” of our past and the development of our culture, by implementing and supporting written sources, stylistic and anthropological studies with molecular data.

Open sesame: Identification of sesame oil and oil soot ink in organic deposits of Tang Dynasty lamps from Astana necropolis in China

Lamp illuminants evidence the exploitation of natural resources, animal and plant domestication, commerce, religious practices and nutrition of ancient populations. However, the physicochemical analysis of their major constituent—burned, degraded and aged mixture of triacylglycerols is imprecise and may lead to ambiguous interpretations. We applied proteomics to analyze fuel deposits from eight lamps dated by 6^th to 8^th centuries AD that were excavated at the Astana necropolis (Xinjiang, China) and determined their origin by identifying organism-specific proteins. Proteomics evidence corroborated and detailed the assignments of source organism relying upon comparative profiling of intact triacylglycerols by shotgun lipidomics. We found that ruminant (mostly, sheep) fat, cattle ghee and sesame oil were common combustibles in Astana and concluded that sesame as an oilseed appeared in China under Tang Dynasty concomitantly with the expansion of Buddhism.

Immunochemical Methods Applied to Art-Historical Materials: Identification and Localization of Proteins by ELISA and IFM

Despite the large diffusion of natural organic substances in art-historical materials, their characterization presents many challenges due to the chemical complexity and instability with respect to degradation processes. Among natural products, proteins have been largely used in the past as binders but also as adhesives or additives in coating layers. Nevertheless, biological identification of proteins in art-historical objects is one of the most recent achievements obtained in heritage science thanks to the development of specifically tailored bio-analytical strategies. In the context of this active emerging discipline, immunological methods stand out for sensitivity, specificity and versatility for both protein recognition and localization in micro-samples. Furthermore, the growing use of immunological techniques for advanced diagnostics and clinical applications ensures continuous improvement in their analytical performance. Considering such, this review provides an overview of the most recent applications of enzyme linked immunosorbent assay and immunofluorescence microscopy techniques in the field of heritage materials. Specifically, the main strengths and potentials of the two techniques as well as their limits and drawbacks are presented and discussed herein.

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

RATIONALE

Much credence has been given in the paleoproteomic community to glutamine deamidation as a proxy for the age of proteins derived from fossil and subfossil material, and this modification has been invoked as a means for determining the endogeneity of molecules recovered from very old fossil specimens.

METHODS

We re-evaluated the relationship between glutamine deamidation and geologic time by examining previously published data from five recent mass spectrometry studies of archeaological fossils. Deamidation values recovered for fossils were graphed against their reported chronologic age using WebPlotDigitizer.

RESULTS

The experimental data that has been produced from fossil material to date show that the extent of glutamine deamidation does not correspond to the absolute age of the specimens being examined, but rather show extreme variation between specimens of similar age and taxonomic affinity.

CONCLUSIONS

Because deamidation rates and levels can be greatly affected by numerous chemical and environmental factors, we propose that glutamine deamidation is better suited as an indicator of preservational quality and/or environmental conditions than a mark of the endogeneity or authenticity of ancient proteins.

Circularly polarized luminescence reveals interaction between commercial stains and protein matrices used in paintings

Here we show that circularly polarized luminescence (CPL) can give unique insight into interactions between fluorescent commercial stains and protein-based materials used in painting. CPL can complement information from ECD and fluorescence.

Evaluation of mass spectrometric data using principal component analysis for determination of the effects of organic lakes on protein binder identification

Matrix-assisted laser desorption/ionisation-time of flight (MALDI-TOF) mass spectrometry is commonly used for the identification of proteinaceous binders and their mixtures in artworks. The determination of protein binders is based on a comparison between the m/z values of tryptic peptides in the unknown sample and a reference one (egg, casein, animal glues etc.), but this method has greater potential to study changes due to ageing and the influence of organic/inorganic components on protein identification. However, it is necessary to then carry out statistical evaluation on the obtained data. Before now, it has been complicated to routinely convert the mass spectrometric data into a statistical programme, to extract and match the appropriate peaks. Only several 'homemade' computer programmes without user-friendly interfaces are available for these purposes. In this paper, we would like to present our completely new, publically available, non-commercial software, ms-alone and multiMS-toolbox, for principal component analyses of MALDI-TOF MS data for R software, and their application to the study of the influence of heterogeneous matrices (organic lakes) for protein identification. Using this new software, we determined the main factors that influence the protein analyses of artificially aged model mixtures of organic lakes and fish glue, prepared according to historical recipes that were used for book illumination, using MALDI-TOF peptide mass mapping.

Deamidation of Human γS-Crystallin Increases Attractive Protein Interactions: Implications for Cataract

Deamidation of proteins is one of the most prevalent post-translational modifications found upon aging, and in age-onset diseases. Specific asparagine and glutamine residues are often selectively deamidated during this process. In the human lens, deamidation has been shown to occur in many crystallins, but it is not clear how these deamidated proteins lead to lens opacity or cataract. Here we have modeled in vitro the effect of deamidation of specific asparagine and glutamine residues in human recombinant γS-crystallin (HGS) on the solution properties of the protein. The residues selected for deamidation in vitro are those that are found to be deamidated in aged and cataractous lenses in vivo. Two derivatives were prepared, one with Asn76 and Asn143 deamidated (2N-HGS) and the other with two additional Gln residues (92 and 120) deamidated (2N2Q-HGS). Isoelectric focusing measurements showed the expected lowering of the pI from 6.9 in HGS to ∼6.5 in 2N-HGS and to ∼6.1 in 2N2Q-HGS. However, spectroscopic studies showed no significant change in the secondary and tertiary structures of the deamidated proteins relative to the wild type. The stability of 2N-HGS and 2N2Q-HGS, as measured by guanidinium hydrochloride unfolding, also remained comparable to that of HGS. The main difference was the altered protein-protein interaction among the three proteins. The net repulsive interactions that are characteristic of HGS are diminished in the deamidated derivatives as evidenced by static light scattering measurements of the second virial coefficient, B2 (B2 values for HGS, 2N-HGS, and 2N2Q-HGS of 8.90 × 10(-4), 7.10 × 10(-4), and 6.65 × 10(-4) mL mol g(-2), respectively). Further substantiation is provided by estimates of the excess binding energy of protein-protein interactions in the condensed phase, obtained from measurements of the PEG-induced liquid-liquid phase separation profiles for the three proteins. The data suggest that enhanced attractive protein-protein interactions, arising from the deamidation of HGS, promote protein aggregation, thereby leading to increased light scattering and opacity over time.

Electrospray ionization linear trap quadrupole Orbitrap in analysis of old tempera paintings: application to nineteenth-century Orthodox icons

Proteomic approach in combination with mass spectrometry demonstrates a great potential for identification of proteinaceous materials in works of art. In this study we used a linear trap quadrupole Orbitrap (LTQ-Orbitrap), a state-of-the-art mass spectrometer for parts per million accuracy analyses of peptides behind tryptic hydrolysis. After the efficiency of the proteomic method was confirmed for reference and model samples, micro-samples from historical paintings were for the first time analysed using this technique. Superior performances of the liquid chromatography-mass spectrometry approach using a LTQ-Orbitrap mass spectrometer allowed identification of egg yolk peptides in two samples from nineteenth-century Orthodox icons, indicating egg tempera as the painting technique. Accurate precursor ion masses, in the range of ±2 ppm, and retention times of tryptic peptides strengthen protein identification. Additionally, in all historical samples the presence of animal glues suggested that the ground layer was likely bound using bovine collagen. Comparing to results acquired using matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry in our previous study, here we achieved higher ion scores and protein scores, better sequence coverage and more identified proteins. In fact, a combination of the two mass spectrometric techniques provided overlapping and complementary data, related to the detection of peptides with different physicochemical properties.

Proteomics identifies the composition and manufacturing recipe of the 2500-year old sourdough bread from Subeixi cemetery in China

We report on the geLC-MS/MS proteomics analysis of cereals and cereal food excavated in Subeixi cemetery (500-300BC) in Xinjiang, China. Proteomics provided direct evidence that at the Subexi sourdough bread was made from barley and broomcorn millet by leavening with a renewable starter comprising baker's yeast and lactic acid bacteria. The baking recipe and flour composition indicated that barley and millet bread belonged to the staple food already in the first millennium BC and suggested the role of Turpan basin as a major route for cultural communication between Western and Eastern Eurasia in antiquity. This article is part of a Special Issue entitled: Proteomics of non-model organisms.

BIOLOGICAL SIGNIFICANCE

We demonstrate that organic residues of thousand year old foods unearthed by archeological excavations can be analyzed by geLC-MS/MS proteomics with good representation of protein source organisms and coverage of sequences of identified proteins. In-depth look into the foods proteome identifies the food type and its individual ingredients, reveals ancient food processing technologies, projects their social and economic impact and provides evidence of intercultural communication between ancient populations. Proteomics analysis of ancient organic residues is direct, quantitative and informative and therefore has the potential to develop into a valuable, generally applicable tool in archaeometry. This article is part of a Special Issue entitled: Proteomics of non-model organisms.

Interactions between inorganic pigments and proteinaceous binders in reference paint reconstructions

The degradation of the proteinaceous binders, ovalbumin (OVA) and casein, and their interactions with azurite (Cu(3)(CO(3))(2)(OH)(2)), calcium carbonate (CaCO(3)), hematite (Fe(2)O(3)) and red lead (Pb(3)O(4)) pigments were studied. A multi-analytical approach based on Thermogravimetric Analysis (TG), Differential Scanning Calorimetry (DSC), Fourier Transform Infrared Spectroscopy (FTIR) and Size Exclusion Chromatography (SEC) was used. The research was carried out on a set of paint reconstructions, which were analysed before and after artificial light ageing. We highlighted that in most cases the inorganic pigments interact with both proteins by decreasing their thermal stability and their intermolecular β-sheet content, and that ageing induces aggregation. We hypothesized that pigments intercalate between protein molecules, producing a partial disruption to the protein-protein intermolecular interaction. In the case of casein, these phenomena continued during ageing. In fact, we observed a complete disappearance of intermolecular β-sheets and an increase in intramolecular β-sheets and random coil during ageing. This result is in agreement with the structural properties of casein, whose aggregation is known to be induced by hydrophobic interactions. On the other hand, in aged OVA paint replicas, we observed the formation of new intermolecular β-sheets and an increase in thermostability. In addition FTIR showed oxidation of the side chains of the aged OVA/hematite sample and aged casein pigment samples, and SEC highlighted hydrolysis phenomena in aged carbonate, azurite and red lead/OVA complexes and in aged casein/calcium carbonate and casein/azurite samples.

Paleoproteomic study of the Iceman's brain tissue

The Tyrolean Iceman, a Copper-age ice mummy, is one of the best-studied human individuals. While the genome of the Iceman has largely been decoded, tissue-specific proteomes have not yet been investigated. We studied the proteome of two distinct brain samples using gel-based and liquid chromatography-mass spectrometry-based proteomics technologies together with a multiple-databases and -search algorithms-driven data-analysis approach. Thereby, we identified a total of 502 different proteins. Of these, 41 proteins are known to be highly abundant in brain tissue and 9 are even specifically expressed in the brain. Furthermore, we found 10 proteins related to blood and coagulation. An enrichment analysis revealed a significant accumulation of proteins related to stress response and wound healing. Together with atomic force microscope scans, indicating clustered blood cells, our data reopens former discussions about a possible injury of the Iceman's head near the site where the tissue samples have been extracted.