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Peptides are known for their diverse bioactivities including antioxidant, antimicrobial, and anticancer activity, all three of which are potentially useful in treating colon-associated diseases. Beside their capability to stimulate positive health effects once released in the body, peptides are able to form useful nanostructures such as hydrogels. Combining peptide bioactivity and peptide gel-forming potentials can create interesting systems that can be used for oral delivery. This combination, acting as a two-in-one system, has the potential to avoid the need for delicate entrapment of a drug or natural bioactive compound. We here review the context and research progress, to date, in this area.

The properties of milk proteins differ between mammalian species. β-Lactoglobulin (βlg) proteins from caprine and bovine milk are sequentially and structurally highly similar, yet their physicochemical properties differ, particularly in response to pH. To resolve this conundrum, we compared the dynamics of both the monomeric and dimeric states for each homologue at pH 6.9 and 7.5 using hydrogen/deuterium exchange experiments. At pH 7.5, the rate of exchange is similar across both homologues, but at pH 6.9 the dimeric states of the bovine βlg B variant homologue have significantly more conformational flexibility compared with caprine βlg. Molecular dynamics simulations provide a mechanistic rationale for the experimental observations, revealing that variant-specific substitutions encode different conformational ensembles with different dynamic properties consistent with the hydrogen/deuterium exchange experiments. Understanding the dynamic differences across βlg homologues is essential to understand the different responses of these milks to processing, human digestion, and differences in immunogenicity.

Human hair is regularly subjected to chemical and physical insults, such as heat, UV-irradiation and alkaline hair care products. These insults result in molecular modifications at the hair protein level that underpin mechanical and sensory property changes in the fibres. These changes can manifest itself in reduced hair quality and performance attributes observable to the consumer. In this work, changes in protein modification as a result of heat and alkaline treatments are determined.Redox proteomic profiling using high-resolution mass spectrometry was applied to map and evaluate amino acid residue modifications in human hair exposed to a combination of thermal treatments and alkali exposure with the aim to understand the underlying chemical processes.Our results show that an increase in redox-related modifications is associated with exposure to higher levels of hydrothermal and alkaline insult. Post-translational modification profiling at the protein primary structural level delivered some further insights into the site-specificity of these modifications, with a clear increase in the number of cysteic acid modifications noticed in samples subjected to more extreme insults.Pinpointing modification sides within proteins and the hair shaft proteome can be used as a basis for employing mitigation or repair strategies of hair protein damage caused by environmental or hair treatment-related insults.Les cheveux humains sont sujet à de nombreuses agressions physiques et chimiques telles que la chaleur, les radiations ultra-violettes et les produits alcalins d’entretien des cheveux. Ces agressions entrainent des modifications moléculaires dans les protéines constituant les cheveux et elles conduisent aussi à des changements mécaniques et sensoriels des fibres capillaires. Les manifestations possibles de ces transformations sont une baisse, visible pour le consommateur, de la qualité et des indicateurs de performance des cheveux. Lors de cette étude, nous mettons en évidence les changements au niveau protéique liés à la chaleur et aux traitements alcalins. MÉTHODES: Les méthodes de profilage d’oxydoréduction protéomique utilisant des spectromètres de masses à haute résolution ont été utilisées afin d’évaluer les modifications des amino-acides dans les cheveux humains après exposition à plusieurs combinaisons de traitements thermiques et alcalins dans le but de comprendre les processus chimiques impliqués. RÉSULTATS: Nos résultats montrent que l’augmentation des modifications d’oxydoréduction est associée à des niveaux élevés d’exposition aux traitements thermiques et/ou alcalins. Le profilage des modifications post-translationnelles des structures primaires des protéines ont permis de mieux comprendre les spécificités de ces modifications ; notamment une augmentation nette du nombre des modifications des acides cystéiques liée aux traitements les plus agressifs.Ce travail d’identification des modifications engendrées par les agressions liées aux traitements capillaires ou environnementales peut désormais servir de base pour évaluer et mettre en place des techniques de réduction des risques, protection et de réparation des protéines des cheveux.

We investigated protein modifications that occur during short- and long-term storage of raw, pasteurized, and ultra-high-temperature processed (UHT) milks using RE-HPLC and redox proteomics. The RE-HPLC results show that casein dissociation and whey protein/κ-casein association occurred in both pasteurized and UHT milk. The extent of protein interactions was more pronounced in UHT milk after storage. The redox proteomics analyses show that primary structural level protein modifications were not correlated to processing type on the of day processing but did occur and increase during storage. Methionine oxidation was the most significant type of oxidative modification in all samples, particularly in the caseins. Methionine oxidation increased in the UHT-treated milk samples with longer storage times, especially in the micelle-phase proteins, likely due to the increasing exposure of these proteins as they migrated to the serum phase. Glycated and lactosylated early-stage Maillard reaction products were also found after heat treatment, particularly in UHT-treated milk, with the levels of these products maintained and generally increased with increasing storage time. PRACTICAL APPLICATION: Understanding changes in protein modification during heat processing and storage of liquid milk products may help develop a model to predict the quality and shelf-life stability of heat treated milk products.

Evaluating the interconnecting effects of pH, temperature and time on food proteins is of relevance to food processing, and food functionality. Here we describe a matrix-based approach in which meat proteins were exposed to combinations of these parameters, selected to cover coordinates in a realistic processing space, and analyzed using redox proteomics. Regions within the matrix showing high levels of protein modification were evaluated for oxidative and other modifications. Both pH and temperature, independently, had a significant effect on the oxidative modifications mostly detected in myofibrillar proteins such as myosin and troponin and also collagen. Heat induced pyroglutamic acid formation was exclusively observed in the myofibrillar proteins. Potential interdependencies between pH, temperature and exposure time were evaluated using a 3-way analysis of variance (ANOVA) on protein modification levels to better understand how industry relevant process parameters influence protein quality and function., Food Science; Food Analysis; Food Chemistry; Proteins; Meat processing conditions; Protein modifications; Proteomics

Trichohyalin (TCHH) is a protein found in ovine wool fibres. It is part of the interfilamentous matrix protein and cross-links both to itself and to the keratin intermediate filament proteins. TCHH is also believed to play a role in the regulation of calcium levels within the hair follicle. This study used PCR-single stranded conformational polymorphism (PCR-SSCP) analysis to investigate variation in the ovine TCHH gene (TCHH). Three sequence variants (A, B and C) were detected in 210 New Zealand (NZ) Romney, Merino, Corriedale, Poll Dorset and cross-bred sheep, with frequencies of 59.0%, 36.9% and 4.1%, respectively. Two single nucleotide polymorphisms (SNPs) were identified in these variants, one located in the 3′ region of intron 2 (c.139-14) and the other one located in exon 3 (c.227). The SNP located in the exon is non-synonymous and would result in an amino acid residue change (p.76Ala/Glu). The association between variation in TCHH and wool traits was investigated in a large half-sib family, in which the sire was AB heterozygous. Progeny that inherited A produced wool with lower mean fibre curvature (MFC), than those that inherited B (P = 0.026). No effects on other wool traits were observed. These results suggest that variation in ovine TCHH affects wool curvature.

Novel animal-derived fibers are of interest for the pet food industry. We here introduce a method for extracting wool proteins using controlled hydrolysis of wool. This results in an appropriate form and we demonstrate its application in pet food using the domestic cat. The effect of the wool hydrolysate on biomarkers of digestive health (e.g., fecal short-chain fatty acids and fecal microbial composition, apparent amino acid (AA) and protein digestibility), are also described. In a feeding study, a cohort of cats (n = 8 per treatment) were fed a basal diet (Control), or the basal diet supplemented with 2% wool hydrolysate, 2% inulin (Synergy1; as is) or 2% cellulose (Novagel; as is). The concentration of butyric acid was not significant (P = 0.102) between treatment groups. The concentration of fecal lactic acid was greatest (P = 0.007) in cats on the Novagel diet. Valeric acid was increased (P = 0.001) in cats fed Synergy1. Supplementation of cat diet with a wool hydrolysate showed similarities to Novagel supplementation in terms of its effects on fecal short-chain fatty acid concentrations and fecal microbiota composition. Wool hydrolysate increased apparent cysteine digestibility compared to Synergy 1 or Novogel. In terms of fecal health, intake, and palatability, the diet supplemented with wool hydrolysate was not detrimental, being similar to currently used dietary fiber supplements. These findings indicate that wool hydrolysates offer promise as an animal-derived supplement source for pet diets.

Blanching is an important process in the preparation of navy beans (Phaseolus vulgaris L.) for canning. We here explore the effect of blanching which can profoundly affect protein composition and introduce protein-primary-level modifications. Amino acid analysis showed significantly decreased protein abundance (58.5%) in blanched beans compared to raw beans. Proteomic analyses revealed a decrease in high molecular weight isoforms of the major storage globulin proteins phaseolin (mean fold-change −3.7) and legumin (mean fold-change −2.5) and concomitant increase in their low molecular weight isoforms (mean fold-change 6.4 and 8.3, respectively). Blanched beans also had decreased abundance of lipoxygenase (mean fold-change −13.1), an enzyme responsible for product spoilage during storage. Increased lysinoalanine (up to 47%) and highly modified protein fragments were found in the processing waters, indicating heat- induced modifications. Correlating these molecular level changes thus provides a basis for evaluating how processing parameters can be modified to increase protein food quality.

Raw bovine milk was heated using common industrial heat treatment conditions to determine how treatment conditions modify proteins and lipids. Processing temperature and time were found to affect both the degree and type of molecular modification. An early and consistent protein marker of heating was identified, namely the presence of the Maillard modification (carboxymethyl or carboxyethyl) at the Lys22 residue in the whey protein glycosylation-dependent cell adhesion molecule 1 (GLCM1). Observable chemical protein modifications generally initially increased with increasing temperature but decreased then under more extreme conditions. For lipids, the concentrations of free fatty acids, methylketones, and oxidised fatty acids were directly correlated with pasteurisation temperature. However, mirroring the trend for protein modification, phosphatidylcholine hydroperoxide levels first increased and then decreased at higher temperature. These protein and lipid modifications are potential markers of milk modification during processing and product development.

It has long been recognised that there are differences between human milk and infant formulas which lead to differences in health and nutrition for the neonate. In this study we examine and compare the peptide profile of human milk and an exemplar infant formula. The study identifies both similarities and differences in the endogenous and postdigestion peptide profiles of human milk and infant formula. This includes differences in the protein source of these peptides but also with the region within the protein producing the dominant proteins. Clustering of similar peptides around regions of high sequence identity and known bioactivity was also observed. Together the data may explain some of the functional differences between human milk and infant formula, while identifying some aspects of conserved function between bovine and human milks which contribute to the effectiveness of modern infant formula as a substitute for human milk.

Oxidative damage significantly affects the food industry, with progressive modification of protein foods and ingredients altering structure, shelf-life, digestibility, nutritional value and function. A redox proteomic damage scoring system was applied to profile and track protein primary level photo-oxidative modification in UVB-irradiated bovine milk whey proteins, lactoferrin and β-lactoglobulin. Lactoferrin oxidation increased significantly after ultraviolet B (UVB) exposure, with the redox score increasing from 0.38 in the control to 1.00 in the irradiated sample. β-lactoglobulin oxidation also increased significantly, from a relatively high baseline redox score of 1.07 in the control to 1.67 in the irradiated sample. A potential marker peptides set for tracking photo-oxidation in milk whey proteins was characterised, with six lactoferrin and four β-lactoglobulin peptides identified. This is anticipated to be of significant utility in monitoring and tracking relative levels of modification, and therefore exposure to oxidative insult, in dairy products through processing, storage, and retail and consumer handling.

Collagens are large structural proteins that are prevalent in mammalian connective tissue. Peptides designed to include a glycine-proline-hydroxyproline (GPO) amino acid triad are biomimetic analogs of the collagen triple helix, a fold that is a hallmark of collagen-like sequences. To inform the rational engineering of collagen-like peptides and proteins for food systems, we report the crystal structure of the (GPO)

Food ingredients commonly undergo heat treatment. Meat, in particular, is typically consumed after some form of heating, such as boiling or roasting. Heating of meat can introduce a wide range of structural changes in its proteinaceous components. At the 3-dimensional structural level, meat proteins may denature and form aggregates upon heating. At the molecular level, primary structure (amino acid residue) alterations reported in cooked meat include protein carbonylation, modification of aromatic residues, and the formation of Maillard reaction products. Identification of these modifications is essential for determining the mechanism of thermal processing of meat and allowing better control of the nutritional and functional properties of products. This article reviews and summarizes the current state of understanding of protein modifications at the molecular level in commonly consumed mammalian food. In addition, relevant case studies relating to characterization of heat-induced amino acid residue-level modifications in other biological materials such as milk and wool are discussed to provide complementary insights.

Four muscles from New Zealand-raised Angus steers were evaluated (musculus semitendinosus, m. longissimus thoracis et lumborum, m. psoas major and m. infraspinatus) to test their differences and common features in protein and peptide abundances. The ultimate goal of such a comparison is to match muscle types to products with targeted properties. Protein profiling based on two-dimensional electrophoresis showed that the overall profiles were similar, but, between muscle types, significant (p0.05) intensity differences were observed in twenty four protein spots. Profiling of endogenous peptides allowed characterisation of 346 peptides. Quantitative analysis showed a clear distinction between the muscle types. Forty-four peptides were identified that showed a statistically significant (p0.05) and substantial (2-fold change) difference between at least two muscle types. These analyses demonstrate substantial similarities between these four muscle types, but also clear distinctions in their profiles; specifically a 25% difference between at least two muscles at the peptidomic level, and a 14% difference at the proteomic level.

Lactoferrin and β-lactoglobulin are important protein components of mammalian milk. Maillard reactions, as well as redox chemistry, are of particular interest for dairy products because they are known to occur during common processing steps, notably heating procedures such as pasteurization. Using a redox proteomics approach, we characterized AA residue side-chain modification across a range of heating times and with or without the specific addition of lactose, to both map the key modification sites within these proteins and evaluate their sensitivity to process-induced modification. Heating in the presence of lactose resulted in significant Maillard modification (both lactosylation and carboxymethylation) to both bovine lactoferrin and β-lactoglobulin. Notably, Lys47, a key residue in the bioactive peptide lactoferricin, was particularly susceptible to modification. Lactoferrin appeared to be fairly robust to hydrothermal treatment, with relatively low levels of oxidative modification observed. In contrast, β-lactoglobulin was susceptible to significant oxidative modification under hydrothermal treatment, with the range and type of modifications observed suggesting compromised nutritional value. These results have important implications for processing applications in dairy foods where retention of biological function and optimal protein quality is desired.

Human hairs are subject to oxidative modification when exposed to sunlight. In the present study, samples of human hair from Chinese volunteers that included frequent hair dyers and non-dyers were analyzed for metal ions such as iron, copper, magnesium, aluminum, zinc and lead. The generation of hydroxyl radicals during UVA (315-400 nm) photoageing was quantified and oxidative damages characterized by proteomic and SEM analysis. It was concluded that high levels of metal ions, particularly those derived from iron and copper, identified in the dyed hairs are associated with enhanced photoformation of hydroxyl radicals and resultant photooxidative damage of the hair. Reactive oxygen species, including hydroxyl radicals, generated via an electron transfer mechanism with hair photosensitizers react with hair proteins. Proteomic analysis of hair samples from frequent hair dyers, regardless of age and gender, showed an almost 1.6 fold increase in the protein oxidative modification levels compared to the undyed samples. As a result, a more pronounced physical damage including fragmentation and cross-linkage of cuticle scales was observed on the surface of dyed hair samples during the photoageing. This work is aimed at better understanding the role of metal ions in dyed hairs and their possible role in photosensitizing hair proteins. The results from this study are anticipated to contribute to the improved development of hair coloring cosmetics and hair care products.

The poultry meat processing industry produces large amounts of feather meal, which is traditionally used as lowvalue plant fertilizer or fish nutrient. A higher value application for feather meal is described in this paper - a thermal blending and compression molding method to create compostable composites out of environmentally friendly materials: feather meal, glycerol, and a biodegradable copolymer of methyl vinyl ether and maleic anhydride (MVEMA). The composite’s mechanical, microstructural and chemical characteristics are described. Feather meal plasticized only with glycerol is mechanically fragile, with average tensile strength of 1.7 MPa, Young’s modulus of 296 MPa and strain-at-failure of 0.6 %. With the addition of MVEMA copolymer, feather meal is transformed into a ductile plastic composite, with tensile modulus reduced 2- to 5-fold and strain-at-failure increased 4- to 25-fold. These properties are ideal for creating feather mealbased compostable bioplastics for agricultural and industrial applications.

Fungal endophytes belonging to the genus Epichloë form associations with temperate grasses belonging to the sub-family Poöideae that range from mutualistic through to pathogenic. We previously identified a novel endophyte gene (designated gigA for grass induced gene) that is one of the most abundantly expressed fungal transcripts in endophyte-infected grasses and which is distributed and highly expressed in a wide range of Epichloë grass associations. Molecular and biochemical analyses indicate that gigA encodes a small secreted protein containing an imperfect 27 amino acid repeat that includes a kexin protease cleavage site. Kexin processing of GigA liberates within the plant multiple related products, named here as epichloëcyclins, which we have demonstrated by MS/MS to be cyclic peptidic in nature. Gene deletion of gigA leads to the elimination of all epichloëcyclins with no conspicuous phenotypic impact on the host grass, suggesting a possible bioactive role. This is a further example of a ribosomal peptide synthetic (RiPS) pathway operating within the Ascomycetes, and is the first description of such a pathway from a mutualistic symbiotic fungus from this Phylum.

Collagens are large structural proteins that are prevalent in mammalian connective tissue. Peptides designed to include a glycine-proline-hydroxyproline (GPO) amino acid triad are biomimetic analogs of the collagen triple helix, a fold that is a hallmark of collagen-like sequences. To inform the rational engineering of collagen-like peptides and proteins for food systems, we report the crystal structure of the (GPO)10 peptide at 0.89-A resolution, solved using direct methods. We determined that a single chain in the asymmetric unit forms a pseudo-hexagonal network of triple helices that have a pitch variation consistent with the model 7/2 helix (3.5 residues per turn). The proline rings occupied one of two states, while the helix was found to have a well-defined hydration shell involved in the stabilization of the inter-helix crystal network. This structure offers a new high-resolution basis for understanding the hierarchical assembly of native collagens, which will aid the food industry in engineering new sustainable food systems.

Oxidation of keratin results in a range of deleterious effects, including discolouration and compromised physical and mechanical properties. Keratin oxidative degradation is driven by molecular-level events, with accumulation of modifications at the protein primary level resulting directly in changes to secondary, tertiary and quaternary structure, as well as eventually changes in the observable physical and chemical properties. Advances in proteomic analysis techniques provide an increasingly clearer insight into the cascade of molecular modification underpinning keratin oxidation and how this translates through to higher order changes in properties. This chapter summarises the effects of oxidation on keratin-based materials, the types of molecular modification associated with this, and advances in techniques and approaches for characterising this modification.

Oxidation of keratin results in a range of deleterious effects, including discolouration and compromised physical and mechanical properties. Keratin oxidative degradation is driven by molecular-level events, with accumulation of modifications at the protein primary level resulting directly in changes to secondary, tertiary and quaternary structure, as well as eventually changes in the observable physical and chemical properties. Advances in proteomic analysis techniques provide an increasingly clearer insight into the cascade of molecular modification underpinning keratin oxidation and how this translates through to higher order changes in properties. This chapter summarises the effects of oxidation on keratin-based materials, the types of molecular modification associated with this, and advances in techniques and approaches for characterising this modification.

The hair follicles of most mammals are of two types, primary and secondary. Primary follicles develop earlier and have a prominent arrectorpili muscle. Secondary follicles have less prominent muscles and are often clumped, sharing a common opening from which fibres emerge. It is not entirely clear what types of follicles occur in human scalps. Partly this is because human hairs have a uniform appearance, unlike many mammals in which robust primary hairs differ markedly from narrow secondary fibres. Some sheep breeds are an exception because like humans, wool fibres have a similar macro-scale appearance irrespective of follicle type. How deep does this similarity go? Using electron microscopy, we examined wool primary fibres from different breeds and contrasted them to secondary fibres. For fibres of similar diameter, there was no significant difference in the ultrastructure or proportion and distribution of cortex cell types in primary and secondary fibres. We conclude that fibre diameter is the most important fibre parameter with respect to structural differences between fibres, not whether the fibres originate from primary or secondary follicles.

Most archaeological and historical textiles (clothing, tapestries, blankets, carpets, etc.) present traces of UV-induced damage when exposed to light during their lifetime. Yellowing of the fibres, fading of the dyes and loss of physical properties, such as tensile strength are the typical indicators of photodegradation. Natural fibres made of proteins, such as wool and silk are particularly sensitive to UV damage. Photo-oxidative damage is caused by the accumulation of chemical modification at the amino acid residue level that lead to a range of oxidation products, including chromophores responsible for changes in coloration, as well as to the breaking of peptide bonds in the protein backbone. Amino acid residues with aromatic side-chain groups are particularly sensitive to photo-oxidation and breakthroughs have been made in recent years in the field of protein science to identify the photoproducts and locate them within proteins. This study explores new methodologies using redox proteomics-based strategies to assess the extent of photodamage in ancient wool textiles, by identifying modifications occurring at the molecular level. Using a scoring system to determine the level of oxidation in amino acids with aromatic side-chains (tryptophan, tyrosine, histidine and phenylalanine), we compare the effects of dyes and mordants on fibres after UV ageing, and assess the extent of oxidation on the different proteins composing the wool fibres. We determine that dyes and mordants have the capability of slowing down photo-oxidation during ageing. We also assess the effect of UV irradiation on deamidation, a modification targeting glutamine and asparagine, as it is a common marker of ageing in ancient proteins.

The cuticle plays an important role in determining characteristic traits of wool fibres, but little is known about the identity and abundance of its proteinaceous constituents and whether there are unique differences in cuticle composition of wools from different breeds of sheep. In this study, protein profiles of enriched endocuticle fractions from fine (Merino), strong (Romney) wool and a sheep that sheds its wool (Wiltshire) were determined by LC-MS/MS and LC-MALDI, quantitative differences being determined by iTRAQ-labelling. Although keratin composition of the cuticle was similar between breeds, with the exception of K82, there were clear differences in the number of identified keratin-associated proteins. Overall, both qualitative and quantitative differences in protein composition of the cuticle from different sheep breeds were found, which may contribute to the unique characteristics of these wools.

The impact of variation in KRTAP1-2 on wool traits was investigated in 383 Merino cross sheep, sired by six different rams. DNA samples from these sheep were genotyped at KRTAP1-2 using PCR-single strand conformational polymorphism (PCR-SSCP) analysis. Seven previously reported gene variants (A–C, E–H) and two newly identified variants (J and K) were detected, with a frequency of 25.5%, 10.3%, 1.4%, 0.1%, 39.4%, 12.8%, 9.1%, 0.4% and 0.3%, respectively. The effects of variants E, J and K on wool traits were not investigated as they were found at a very low frequency. Of the other six variants; A, B and C were found to be associated with a number of wool traits, but the strongest association was with three correlated traits clean fleece weight (CFW), greasy fleece weight (GFW) and yield. The presence of A was associated with an increase in GFW, CFW and yield. The presence of B was also associated with an increase in GFW, CFW and yield. The presence of C was associated with a decrease in GFW and CFW, but increased yield. Genotypes AF and AG had a higher GFW than FG and FH; AF and AG had a higher CFW than FG; and sheep of AF, AG and BF had a higher yield than those of FF and FG. These results suggest that consideration of ovine KRTAP1-2 may be useful when developing breeding programs based on wool weight.

In this work egg white was used to study the effect of common food processing conditions on in vitro protein digestibility and on the modification of amino acid residues. Egg white was treated at 20 °C and 100 °C, varying pH (2–12), and zero and high-salt concentrations (0 mM, 200 mM). The digestibility assays confirmed previous findings that exposure of egg white to high temperatures increased digestibility markedly. However, the effects of pH and salt concentrations were found to be minimal. Proteomic analysis was utilised to map amino acid modifications, revealing that increased digestibility in heated egg white comes at the cost of a higher degree of amino acid residue-level modification. The predominant modifications were found to be dehydration and deamidation reactions that increased with increasing heat exposure time. The effects of the Maillard reaction on digestibility and amino acid modification were also determined for egg white in the presence of glucose and methylglyoxal. Proteomic assessment clearly revealed a high degree of modification of up to 38% of available arginine residues in the presence of methylglyoxal. An important correlation was therefore established between increased levels of Maillard reaction products and a decrease in the nutritional value of egg white.

This Data article provides Supplementary data related to the research article titled “In-depth characterisation of the lamb meat proteome from longissimus lumborum ” by Yu et al. [1] . This research article reports the proteome catalogue of the 48 h post-mortem lamb longissimus lumborum. A list of 388 ovine-specific proteins were identified and characterised after separating the samples into sarcoplasmic, myofibrillar and insoluble fractions, followed by an in-depth shotgun proteomic evaluation and bioinformatic analysis. The detailed list of identified proteins, the annotated MS/MS spectra corresponding to the proteins identified by a single peptide-spectrum match, the raw Gene Ontology annotation data and other miscellaneous files, as will be described below, were contained in this Data article. We hope the data presented here will contribute to the current knowledge of the global protein composition of lamb skeletal muscle/meat.

The disulfide bond network within the cortex of mammalian hair has a critical influence on the physical and mechanical characteristics of the fiber. The location, pattern, and accessibility of free and crosslinked cysteines underpin the properties of this network, but have been very difficult to map and understand, because traditional protein extraction techniques require the disruption of these disulfide bonds. Cysteine accessibility in both trichocyte keratins and keratin associated proteins (KAPs) of wool was investigated using staged labeling, where reductants and chaotropic agents were used to expose cysteines in a stepwise fashion according to their accessibility. Cysteines thus exposed were labeled with distinguishable alkylation agents. Proteomic profiling was used to map peptide modifications and thereby explore the role of KAPs in crosslinking keratins. Labeled cysteines from KAPs were detected when wool was extracted with reductant only. Among them were sequences from the end domains of KAPs, indicating that those cysteines were easily accessible in the fiber and could be involved in forming interdisulfide linkages with keratins or with other KAPs. Some of the identified peptides were from the rod domains of Types I and II keratins, with their cysteines positioned on the exposed surface of the α-helix. Peptides were also identified from keratin head and tail domains, demonstrating that they are not buried within the filament structure and, hence, have a possible role in forming disulfide linkages. From this study, a deeper understanding of the accessibility and potential reactivity of cysteine residues in the wool fiber cortex was obtained.

Hair curvature underpins structural diversity and function in mammalian coats, but what causes curl in keratin hair fibres? To obtain structural data to determine one aspect of this question, we used confocal microscopy to provide in situ measurements of the two cell types that make up the cortex of merino wool fibres, which was chosen as a well-characterised model system representative of narrow diameter hairs, such as underhairs. We measured orthocortical and paracortical cross-sectional areas, and cortical cell lengths, within individual fibre snippets of defined uniplanar curvature. This allowed a direct test of two long-standing theories of the mechanism of curvature in hairs. We found evidence contradicting the theory that curvature results from there being more cells on the side of the fibre closest to the outside, or convex edge, of curvature. In all cases, the orthocortical cells close to the outside of curvature were longer than paracortical cells close to the inside of the curvature, which supports the theory that curvature is underpinned by differences in cell type length. However, the latter theory also implies that, for all fibres, curvature should correlate with the proportions of orthocortical and paracortical cells, and we found no evidence for this. In merino wool, it appears that the absolute length of cells of each type and proportion of cells varies from fibre to fibre, and only the difference between the length of the two cell types is important. Implications for curvature in higher diameter hairs, such as guard hairs and those on the human scalp, are discussed.

In several biomedical research fields, the cross-linking of peptides and proteins has an important impact on health and wellbeing. It is therefore of crucial importance to study this class of post-translational modifications in detail. The huge potential of mass spectrometric technologies in the mapping of these protein-protein cross-links is however overshadowed by the challenges that the field has to overcome. Areas covered: In this review, we summarize the different pitfalls and challenges that the protein-protein cross-linking field is confronted with when using mass spectrometry approaches. We additionally focus on native disulfide bridges as an example and provide some examples of cross-links that are important in the biomedical field. Expert commentary: The current flow of methodological improvements, mainly from the chemical cross-linking field, has delivered a significant contribution to deciphering native and insult-induced cross-links. Although an automated data analysis of proteome-wide peptide cross-linking is currently only possible in chemical cross-linking experiments, the field is well on the way towards a more automated analysis of native and insult-induced cross-links in raw mass spectrometry data that will boost its potential in biomedical applications.

Sol-gel technology offers a promising route to impart new properties to textile substrates. However, relatively little attention has been paid to the effect of precursor concentration in the sol-gel processing on the inherent properties of sol-gel treated textile substrates. In this study, titanium (IV) isopropoxide (TTIP) was used as the precursor material, and colourless TiO2 sol solutions were prepared at three precursor concentrations. Wool fabrics were coated with as-prepared TiO2 sol solutions via a dip-dry-cure technique. The optical, morphological, tensile properties and washing durability of both untreated or sol-gel treated wool fabrics were then evaluated. The results show that TiO2 sol-gel prepared at a relatively higher precursor concentration resulted in a thicker coating and a better UV protection on the treated wool fabric. TTIP precursor concentration also played an important role in the washing durability of TiO2 sol-gel coatings. Both the tensile strength and elongation at break of the treated wool fabrics were largely improved, however the degree of improvement seemed to be less dependent on the precursor concentrations of as-prepared TiO2 sol-gels.

Keratins derived from wool and feathers are a source of raw materials for biomaterial use. Such biomaterials are essentially biodegradable polyamides, and offer many favourable features such as biocompatibility in contrast with petro-derived synthetic materials. In the present study, raw wool samples were dissolved in hot ionic liquid (1-butyl-3-methylimidazolium chloride) at temperatures ranging from 120 to 180 °C, resulting in regenerated keratins after coagulation with water. The physicochemical characteristics of the regenerated keratins were evaluated with respect to their protein profile, thermal stability, mechanical performance and SEM morphology, and contrasted with those of raw wool. Cysteine content reduced significantly on increasing temperature of ionic liquid and some disordering of protein secondary structures occurred in regenerated keratins. Keratin regenerated from a solution prepared with ionic liquid at 180 °C showed improved thermal processing properties, and it revealed dense fibrous network morphology of the film's cross-sectional surface produced under compression moulding. This in-depth study on regenerated keratins demonstrates a potential new route for the conversion of keratinous materials into bio-resin for industrial applications. However, further development is required to create keratinous materials that are melt-processable like classical synthetic polymers.

Human scalp hairs are comprised of a central cortex enveloped by plate-like cuticle cells. The elongate cortex cells of mature fibres are composed primarily of macrofibrils-bundles of hard-keratin intermediate filaments (IFs) chemically cross-linked within a globular protein matrix. In wool, three cell types (ortho-, meso- and paracortex) contain macrofibrils with distinctly different filament arrangements and matrix fractions, but in human hair macrofibril-cell type relationships are less clear. Here we show that hair macrofibrils all have a similar matrix fraction (∼0.4) and are typically composed of a double-twist architecture in which a central IF is surrounded by concentric rings of tangentially-angled IFs. The defining parameter is the incremental angle increase (IF-increment) between IFs of successive rings. Unlike the wool orthocortex, hair double-twist macrofibrils have considerable inter-macrofibril variation in IF increment (0.05-0.35°/nm), and macrofibril size and IF increment are negatively correlated. Correspondingly, angular difference between central and outer-most IFs is up to 40° in small macrofibrils, but only 5-10° in large macrofibrils. Single cells were observed containing mixtures of macrofibrils with different diameters. These new observations advance our understanding of the nano-level and cell-level organisation of human hair, with implications for interpretation of structure with respect the potential roles of cortex cell types in defining the mechanical properties of hair.

Lipid oxidation plays a critical role in the quality of meat and meat products; however, lipid degradation is generally evaluated at a holistic level, without attention to spatial distribution. Marker lipids were selected based on their relative abundance and characteristic MS fragmentation patterns (10 phospholipids, 2 triglycerides, and cholesterol). These markers were subsequently utilised for temporal and spatial profiling of lipid degradation in bovine M. longissimus dorsi lumborum steaks subjected to high (packaged in 80% O2/20% CO2 modified atmosphere), atmospheric (oxygen permeable film) and ultra-low (vacuum-packaged) oxygen packaging during storage through matrix-assisted laser desorption/ionisation time-of-flight/time-of-flight (MALDI–TOF/TOF) mass spectrometric imaging. Interestingly, markers showed highly contrasting effects in terms of their oxidative stability over time. The relative abundance of phophatidylcholines generally declined rapidly under high oxygen conditions. In contrast, PC 18:1/18:0 showed high relatively stability to oxidation. Cholesterol also displayed high relative stability. Overall, high oxygen packing was found to result in rapid lipid degradation, while vacuum-packaging significantly mitigated lipid degradation. Oxidative degradation profiles were spatially heterogeneous across meat sub-samples and differences were also observed from the centre and edge of the steaks. This new approach to tracking lipid degradation directly from meat samples offers increasingly precise tracking of modification in meat and other foods.

Investigations into the use of the ionic liquid 1-butyl-3-methylimidazolium chloride [BMIM]+[Cl]− to extend the mapping of the wool proteome have established that it is complementary to the use of commonly used chaotropic agents such as urea. Extraction of proteins from wool is challenging with only 50–60% extraction possible by traditional methods that utilise chaotropes in the presence of a reducing agent. Incubation of wool at high temperatures in the presence of [BMIM]+[Cl]− resulted in large scale disruption of the fibre into cells and sub-cellular fragments. The combination of the proteins identified from the ionic liquid treated wool which was subsequently extracted with urea/thiourea and those identified by urea/thiourea extraction alone resulted in the identification of a larger set of proteins from the wool fibre than would have been found by either method alone. Wool proteins, in particular some trichocyte keratins, were uniquely identified with the ionic liquid/(urea/thiourea) combination, while others such as some of the keratin associated proteins were unique to urea/thiourea alone. We conclude that the ionic liquid/(urea/thiourea) method provides complementary coverage of the wool proteome when run alongside the traditional urea/thiourea method.

The extent to which nutritional and functional benefit is derived from proteins in food is related to its breakdown and digestion in the body after consumption. Further, detailed information about food protein truncation during digestion is critical to understanding and optimising the availability of bioactives, in controlling and limiting allergen release, and in minimising or monitoring the effects of processing and food preparation. However, tracking the complex array of products formed during the digestion of proteins is not easily accomplished using classical proteomics. We here present and develop a novel proteomic approach using isobaric labelling to mapping and tracking protein truncation and peptide release during simulated gastric digestion, using bovine lactoferrin as a model food protein. The relative abundance of related peptides was tracked throughout a digestion time course, and the effect of pasteurisation on peptide release assessed. The new approach to food digestion proteomics developed here therefore appears to be highly suitable not only for tracking the truncation and relative abundance of released peptides during gastric digestion, but also for determining the effects of protein modification on digestibility and potential bioavailability.

Deamidation of glutamine (Q) and asparagine (N) has been recognized as a marker of degradation and aging in ancient proteins. Using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) to study deamidation in wool textiles, we identified eight peptides from α-keratin proteins in sheep wool that could potentially be used to assess the level of degradation. For each chosen peptide, the extent of deamidation was determined by comparing the calculated theoretical distribution with the measured distribution using a genetic algorithm that gives the best fit to the measured distribution. Variations in the levels of deamidation were observed between peptides and in modern wool samples buried for up to 8 years in which deamidation levels were relatively low under short-term burial. In contrast, deamidation was higher in archeological textile fragments from medieval sites ranging from the 9th to 13th century in York (United Kingdom) and Newcastle (United Kingdom) and from the 13th to 16th century in Reykholt (Iceland). Major differences were observed between the British and the Icelandic samples, showing a negative correlation between age of samples and levels of deamidation, but highlighting the effect of local environment. In addition, nanoscale liquid chromatography-electrospray ionization tandem mass spectrometry (nanoLC-ESI-MS/MS) data indicated that deamidation in wool's α-keratin was influenced by primary and higher-order structures. Predominance of deamidation on glutamine rather than asparagine in the archeological samples was attributed to a higher abundance of Q in the α-helical core domain of keratins, neighboring residues and steric hindrance preventing deamidation of N.

Wool is a natural composite fiber, with keratin and keratin-associated proteins as the key molecular components. The outermost surface of wool fibers comprises a hydrophobic lipid layer that can lead to unsatisfactory processing and properties of fabric products. In this study, molecular sieve 5A, a Na + and Ca 2+ exchanged type A zeolite with a 1:1 Si:Al ratio was integrated onto the surface of wool using 3-mercaptopropyl trimethoxy silane. The resultant surface morphology, hydrophilicity and mechanical performance of the treated wool fabrics were then evaluated. Notably, the surface hydrophilicity of wool was observed to increase dramatically. When wool was treated with a dispersion of 2 wt% acetic acid, 2.5 wt% zeolite and 0.3 wt% or more silane, the water contact angle was observed to decrease from an average value of 148° to 0° over a period of approximately 30 s. Scanning electron microscopic imaging indicated good coverage of the wool surface with zeolite particles, with infrared spectroscopic evaluation indicating strong bonding of the dealuminated zeolite to wool keratins. This application of zeolite showed no adverse effects on the tensile and other mechanical properties of the fabric. This study indicates that zeolite-based treatment is a potentially efficient approach to increasing the surface hydrophilicity and modifying other key surface properties of wool and wool fabrics.

Patients with high-grade, serous epithelial ovarian carcinoma (HGSOC) are generally diagnosed with extensive peritoneal metastases, and exhibit 5-year survival rates

The effect of reactive oxidation species (ROS) on tryptophan or tyrosine was investigated by qualitatively determining the major detectable oxidation products generated by hydroxyl radicals, produced by the Fenton process, or singlet oxygen, generated by exposure to green light in the presence of Rose Bengal, on these photosensitive amino acids in synthetic pentapeptides. Based on mass spectrometric analysis it would appear that the hydroxyl radical favours a pathway leading to the formation of tryptophandione-based products from tryptophan. In contrast singlet oxygen attack appears to favour the formation of kynurenine-type products from tryptophan. Specific oxidative products observed proteomically are therefore potentially able to discriminate between predominant ROS-mediated pathways. To validate these findings, a keratin-enriched extract was exposed to UVB light under aqueous conditions. The observation of the conversion of tryptophan to hydroxytryptophan in marker peptides, and the absence of singlet-oxygen specific modifications, suggested that under these conditions oxidative degradation occurred primarily via hydroxyl radical attack. These observations provide the first direct proteomic evidence of the dominant photodegradation pathways in wet wool.

Rationale In ancient and/or damaged artefacts containing keratinous materials, the species of origin of the materials can be difficult to identify through visual examination; therefore, a minimally destructive methodology for species identification is required. While hair fibres from some species have seen substantial characterisation, others such as horn or baleen have received little or no attention, or lack protein sequences allowing formal identification using proteomics techniques. Methods We used the PMF method (Peptide Mass Fingerprinting with matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF-MS)) to catalogue and identify diagnostic peptide markers up to the genus level. Sequences were checked using nanoflow liquid chromatography/electrospray ionisation tandem mass spectrometry (nanoLC/ESI-MS/MS) and unidentified peptides were searched against a theoretical database generated by substituting amino acids in keratin sequences. Results Specific peptides were identified by m/z and sequences characterised whenever possible for a range of species belonging to Bovidae and Camelidae, and for tissues such as baleen and horn. The theoretical database allowed an increase in the number of peptides of up to 10% in species with little genetic information. Conclusions A proteomics approach can successfully identify specific markers for the identification of materials to the genus level, and should be considered when identification by other means is not possible. Identification by PMF is fast, reliable and inexpensive.

Low-molecular-weight organic molecules, such as coumarins and stilbenes, are used commercially as fluorescent whitening agents (FWAs) to mask photoyellowing and to brighten colors in fabrics. FWAs achieve this by radiating extra blue light, thus changing the hue and also adding to the brightness. However, organic FWAs can rapidly photodegrade in the presence of ultraviolet (UV) radiation, exacerbating the yellowing process through a reaction involving singlet oxygen species. Inorganic nanoparticles, on the other hand, can provide a similar brightening effect with the added advantage of photostability. We report a targeted approach in designing new inorganic silicon- and germanium-based nanoparticles, functionalized with hydrophilic (amine) surface terminations as novel inorganic FWAs. When applied on wool, by incorporation in a sol-gel Si matrix, the inorganic FWAs improved brightness properties, demonstrated enhanced photostability toward UV radiation, especially the germanium nanoparticles, and also generated considerably lower levels of reactive oxygen species compared to a commercial stilbene-based organic FWA, Uvitex NFW.