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The techniques of agriculture and animal husbandry at Tell Humeida, a Middle Uruk Period (Late Chalcolithic) site on the middle Syrian Euphrates, were studied using stable isotopes of bone collagen of domestic and wild mammals and from cereal and ruderal plant seeds. Two archaeological campaigns in 2009 and 2011 yielded a small collection of bones, most of which were taxonomically indeterminable. The work had to be interrupted due to the political conflict. The faunal study comprised collagen peptide fingerprinting for taxonomic identification, followed by isotopic analysis. Multiple 14C dating were performed to date the infill to around 3600 cal BC. An isotopic analysis of the sparse plant remains suggested that irrigation and manuring were common practices. Sheep and equids predominated in the faunal assemblage. Sheep grazed on manured soils, and their diet could include millet or another C4 plant, of which, however, no carpological remains were found. The diet of equids differed from that of sheep but also that of other wild ungulates (cervids/gazelles). Their isotopic signatures indicated that they grazed in humid areas, near the watercourse. These finds indicated a settlement that was closely linked to the availability of water, which made it possible to grow crops in an almost desert-like area, and the rearing of sheep. [ABSTRACT FROM AUTHOR]

This review article provides a wide overview of important developments and applications of capillary electromigration methods in the area of peptide mapping of proteins in the period 1997–mid‐2022, including review articles on this topic. It deals with all major aspects of peptide mapping by capillary electromigration methods: i) precleavage sample preparation involving purification, preconcentration, denaturation, reduction and alkylation of protein(s) to be analyzed, ii) generation of peptide fragments by off‐line or on‐line enzymatic and/or chemical cleavage of protein(s), iii) postcleavage preparation of the generated peptide mixture for capillary electromigration separation, iv) separation of the complex peptide mixtures by one‐, two‐ and multidimensional capillary electromigration methods coupled with mass spectrometry detection, and v) a large application of peptide mapping for variable purposes, such as qualitative analysis of monoclonal antibodies and other protein biopharmaceuticals, monitoring of posttranslational modifications, determination of primary structure and investigation of function of proteins in biochemical and clinical research, characterization of proteins of variable origin as well as for protein and peptide identification in proteomic and peptidomic studies. [ABSTRACT FROM AUTHOR]

The techniques of agriculture and animal husbandry at Tell Humeida, a Middle Uruk Period (Late Chalcolithic) site on the middle Syrian Euphrates, were studied using stable isotopes of bone collagen of domestic and wild mammals and from cereal and ruderal plant seeds. Two archaeological campaigns in 2009 and 2011 yielded a small collection of bones, most of which were taxonomically indeterminable. The work had to be interrupted due to the political conflict. The faunal study comprised collagen peptide fingerprinting for taxonomic identification, followed by isotopic analysis. Multiple 14C dating were performed to date the infill to around 3600 cal BC. An isotopic analysis of the sparse plant remains suggested that irrigation and manuring were common practices. Sheep and equids predominated in the faunal assemblage. Sheep grazed on manured soils, and their diet could include millet or another C4 plant, of which, however, no carpological remains were found. The diet of equids differed from that of sheep but also that of other wild ungulates (cervids/gazelles). Their isotopic signatures indicated that they grazed in humid areas, near the watercourse. These finds indicated a settlement that was closely linked to the availability of water, which made it possible to grow crops in an almost desert-like area, and the rearing of sheep.

Proteomic methods and approaches to the detection of tissue-specific and tissue-generating proteins and peptides – which form corrective properties – in studied meat samples and specially developed meat products were successfully tried out in 2016–2017. The methods allow one to confirm protein and peptide authenticity and also detect bio-markers of proteolytic changes in meat after slaughter. The following proteomic techniques were used in the present research: two-dimensional O’Farrell electrophoresis with isoelectrofocusing in ampholin and immobilin pH gradients, the detection of proteins on two-dimensional electrophoregrams by staining with Coomassie R-250 and silver nitrate, and mass spectrometric identification of proteins by means of MALDI-TOF and MS/MS methods. Contractile actomyosin complex proteins, such as myosin light chains and tropomyosins, were the most informative among proteins of species specificity. It is also necessary to mention that earlier experiments allowed us to choose enzymes which play a part in carbohydrate metabolism (glyceraldehyde 3-phosphate dehydrogenase and β-enolase) as markers. In addition to the listed proteins, myoglobins, actins, and several other proteins in horse meat have showed high species specificity and have been detected well. A system of species specificity (authenticity) of meat raw materials was suggested. The system allows the presence of pork, beef, horse, and camel meat to be detected in both raw and heat-treated products if the content is 5% and more. The data has been obtained by means of bioinformatics, а highly useful tool for formulating an algorithm to identify the protein markers for the Atlas “Proteomic profiles of farm animals meat proteins”. “Proteomic profiles of farm animals muscle proteins”.

The aim of this study is to explore differences in the peptidomics of Saccharomyces pastorianus protein hydrolysates treated with different enzymes. Briefly, differences in the peptide fingerprints and active peptides of neutral protease/papain-hydrolyzed S. pastorianus were analyzed using ultra-high performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS) combined with PEAKS Online 1.7 analysis software, Peptide Ranker, and the BIOPEP database. Compared to traditional databases, the PEAKS Online uses de novo sequencing for analysis to obtain oligopeptides smaller than pentapeptides. It provides more comprehensive data of the peptide sample. In this study, enzymatic hydrolysates of S. pastorianus protein were prepared under the optimum conditions of neutral protease and papain respectively. In total, 7221 and 7062 polypeptides were identified in the hydrolysates of neutral protease and papain, respectively; among these polypeptides, 980 were common to the two enzymes. The 6241 and 6082 unique peptides found in the hydrolysates of neutral protease and papain, respectively, indicated that the peptide fingerprints of the two hydrolysates are quite different. Peptide Ranker predicted that 3013 (41.73%) and 3095 (43.83%) peptides were potentially bioactive in the hydrolysates of neutral protease and papain, respectively. According to the BIOPEP database, neutral protease and papain contained 295 and 357 active peptides, respectively; these peptides were mainly composed of angiotensin converting enzyme (ACE) inhibitors and dipeptidyl peptidase IV inhibitors and antioxidant peptides. The number of active peptides in the hydrolysate of papain was higher than that in the hydrolysate of neutral protease, but the total ion intensity of active peptides in the former was lower than that in the latter. This study revealed the influence of protease type on the composition of enzymatic hydrolysates from S. pastorianus protein. The above results provide a reference for the development of functional products of S. pastorianus protein peptides and the high-value utilization of yeast resources.

Abstract: Sea anemones are known to contain a wide diversity of biologically active peptides, mostly unexplored according to recent peptidomic and transcriptomic studies. In the present work, the neurotoxic fractions from the exudates of Stichodactyla helianthus and Bunodosoma granulifera were analyzed by reversed-phase chromatography and mass spectrometry. The first peptide fingerprints of these sea anemones were assessed, revealing the largest number of peptide components (156) so far found in sea anemone species, as well as the richer peptide diversity of B. granulifera in relation to S. helianthus. The transcriptomic analysis of B. granulifera, performed by massive cDNA sequencing with 454 pyrosequencing approach allowed the discovery of five new APETx-like peptides (U-AITX-Bg1a–e – including the full sequences of their precursors for four of them), which together with type 1 sea anemone sodium channel toxins constitute a very distinguishable feature of studied sea anemone species belonging to genus Bunodosoma. The molecular modeling of these new APETx-like peptides showed a distribution of positively charged and aromatic residues in putative contact surfaces as observed in other animal toxins. On the other hand, they also showed variable electrostatic potentials, thus suggesting a docking onto their targeted channels in different spatial orientations. Moreover several crab paralyzing toxins (other than U-AITX-Bg1a–e), which induce a variety of symptoms in crabs, were isolated. Some of them presumably belong to new classes of crab-paralyzing peptide toxins, especially those with molecular masses below 2kDa, which represent the smallest peptide toxins found in sea anemones. [Copyright &y& Elsevier]

Abstract: Food traceability is essential to preserve the identity of unique quality traits against frauds or commercial disputes. Therefore, there is a growing demand of new traceability systems for the collection of information related to units/batches of food ingredients and products. A rapid method based on peptide profiles obtained from tryptic digests of whole wine proteins by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry is described. Reliable peptide fingerprints were obtained for high quality Campania white wines, providing a signature of the finished products. The MALDI spectra revealed the presence of common diagnostic ions, but also evidenced differences between wines. Furthermore, the MALDI-TOF spectral traces were converted into simulated images to obtain a graphical representation of spectra. The resulting “mass codes” constitute a simple tool to display differences between samples, suggesting their potential use as “biological bar codes” for food authenticity and traceability, probably applicable to other classes of certified food products. [Copyright &y& Elsevier]

Proteomic-based approaches, which examine expressed proteins in tissues or cells, have great potential in the elucidation of biological defects in heterogeneous neurodevelopmental disorders such as autism. In this approach, tissue or cellular proteins from control and affected subjects are separated on two-dimensional (2-D) polyacrylamide gel electrophoresis, and those proteins that show marked changes in the concentration between control and affected subjects are identified by mass spectroscopy. This method has been successfully applied in the elucidation of the molecular biological defect in classic late-infantile neuronal ceroid lipofuscinosis (Sleat et al., 1997). Unlike the classical methods of genome-wide screening for chromosomal localization followed by positional cloning, the proteomic approach requires limited number of tissue samples and the study can be completed in a relatively short time. Currently, these methods are available for relatively abundant proteins and generally are not applicable for hydrophobic proteins because 2-D gel electrophoresis is not very effective in the analysis of hydrophobic proteins. The genetic defect results in either total loss of proteins or changes in molecular weight and/or isoelectric point will be detectable by the proteomic method. Because autism is a neurogenetic disorder, brain is the tissue of choice for proteomic study. For an oligogenic disorder such as autism, at least some of the aberrant (genes) proteins may be identified by this technology. [ABSTRACT FROM AUTHOR]