1
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Zhang H, Luo JJ, Wang RL, He XY, Zou HL, Luo HQ, Li NB, Li BL. Electrophoretic Microplate Protein Identification Based on Gold Staining of Molybdenum Disulfide Hydrogels. Anal Chem 2024; 96:10074-10083. [PMID: 38848224 DOI: 10.1021/acs.analchem.4c02074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024]
Abstract
Numerous high-performance nanotechnologies have been developed, but their practical applications are largely restricted by the nanomaterials' low stabilities and high operation complexity in aqueous substrates. Herein, we develop a simple and high-reliability hydrogel-based nanotechnology based on the in situ formation of Au nanoparticles in molybdenum disulfide (MoS2)-doped agarose (MoS2/AG) hydrogels for electrophoresis-integrated microplate protein recognition. After the incubation of MoS2/AG hydrogels in HAuCl4 solutions, MoS2 nanosheets spontaneously reduce Au ions, and the hydrogels are remarkably stained with the color of as-synthetic plasmonic Au hybrid nanomaterials (Au staining). Proteins can precisely mediate the morphologies and optical properties of Au/MoS2 heterostructures in the hydrogels. Consequently, Au staining-based protein recognition is exhibited, and hydrogels ensure the comparable stabilities and sensitivities of protein analysis. In comparison to the fluorescence imaging and dye staining, enhanced sensitivity and recognition performances of proteins are implemented by Au staining. In Au staining, exfoliated MoS2 semiconductors directly guide the oriented growth of plasmonic Au nanostructures in the presence of formaldehyde, showing environment-friendly features. The Au-stained hydrogels merge the synthesis and recognition applications of plasmonic Au nanomaterials. Significantly, the one-step incubation of the electrophoretic hydrogels leads to high simplicity of operation, largely challenging those multiple-step Ag staining routes which were performed with high complexity and formaldehyde toxicity. Due to its toxic-free, simple, and sensitive merits, the Au staining integrated with electrophoresis-based separation and microplate-based high-throughput measurements exhibits highly promising and improved practicality of those developing nanotechnologies and largely facilitates in-depth understanding of biological information.
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Affiliation(s)
- Hang Zhang
- Key Laboratory of Modern Analytical Chemistry, Chongqing Education Commission, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Jun Jiang Luo
- Key Laboratory of Modern Analytical Chemistry, Chongqing Education Commission, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Lan Wang
- Key Laboratory of Modern Analytical Chemistry, Chongqing Education Commission, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Xin Yu He
- Key Laboratory of Modern Analytical Chemistry, Chongqing Education Commission, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Hao Lin Zou
- Key Laboratory of Modern Analytical Chemistry, Chongqing Education Commission, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Hong Qun Luo
- Key Laboratory of Modern Analytical Chemistry, Chongqing Education Commission, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Nian Bing Li
- Key Laboratory of Modern Analytical Chemistry, Chongqing Education Commission, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Bang Lin Li
- Key Laboratory of Modern Analytical Chemistry, Chongqing Education Commission, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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2
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Di Gianvincenzo F, Andersen CK, Filtenborg T, Mackie M, Ernst M, Ramos Madrigal J, Olsen JV, Wadum J, Cappellini E. Proteomic identification of beer brewing products in the ground layer of Danish Golden Age paintings. SCIENCE ADVANCES 2023; 9:eade7686. [PMID: 37224244 DOI: 10.1126/sciadv.ade7686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 04/18/2023] [Indexed: 05/26/2023]
Abstract
The application of mass spectrometry-based proteomics to artworks provides accurate and detailed characterization of protein-based materials used in their production. This is highly valuable to plan conservation strategies and reconstruct the artwork's history. In this work, the proteomic analysis of canvas paintings from the Danish Golden Age led to the confident identification of cereal and yeast proteins in the ground layer. This proteomic profile points to a (by-)product of beer brewing, in agreement with local artists' manuals. The use of this unconventional binder can be connected to the workshops within the Royal Danish Academy of Fine Arts. The mass spectrometric dataset generated from proteomics was also processed with a metabolomics workflow. The spectral matches observed supported the proteomic conclusions, and, in at least one sample, suggested the use of drying oils. These results highlight the value of untargeted proteomics in heritage science, correlating unconventional artistic materials with local culture and practices.
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Affiliation(s)
- Fabiana Di Gianvincenzo
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Veˇna Pot 113, 1000 Ljubljana, Slovenia
| | - Cecil Krarup Andersen
- Royal Danish Academy, Conservation, Philip De Langes Allé 10, 3.15, 1435 Copenhagen, Denmark
| | - Troels Filtenborg
- National Gallery of Denmark, Sølvgade 48-50, 1307 Copenhagen, Denmark
| | - Meaghan Mackie
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Madeleine Ernst
- Section for Clinical Mass Spectrometry, Danish Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Jazmín Ramos Madrigal
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Jesper V Olsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Jørgen Wadum
- Centre for Art Technological Studies and Conservation, National Gallery of Denmark, Sølvgade 48-50, 1307 Copenhagen, Denmark
- Wadum Art Technological Studies, Åløkkevej 24, 2720 Vanløse, Denmark
- Nivaagaard Collection, Gammel Strandvej 2, 2990 Nivå, Denmark
| | - Enrico Cappellini
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
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3
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OFFGEL and GELFrEE fractionation: Novel liquid-phase protein recovery strategies in proteomics studies. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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4
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Spada V, Di Stasio L, Picascia S, Messina B, Gianfrani C, Mamone G, Picariello G. Immunogenic Potential of Beer Types Brewed With Hordeum and Triticum spp. Malt Disclosed by Proteomics. Front Nutr 2020; 7:98. [PMID: 32733911 PMCID: PMC7363779 DOI: 10.3389/fnut.2020.00098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 06/03/2020] [Indexed: 11/13/2022] Open
Abstract
The protein/peptide composition of five beer kinds, including two experimental beer-like products brewed with einkorn (Triticum monococcum), a beer labeled as “gluten-free,” a traditional all-barley malt and a wheat (T. aestivum) containing beer, was characterized with HPLC-ESI MS/MS-based proteomics. To enlarge the characterization of the components, the polypeptides were fractionated according to their molecular size (cut-off 6 kDa). All the beer types contained a variety of polypeptides arising from all the gliadin subfamilies (α-/β-, γ-, and ω-gliadins) able to induce an immune response in celiac disease (CD) patients in addition to a panel of IgE-reactive food allergens. Wheat storage proteins were heavily hydrolyzed in the beer samples brewed with einkorn. The presence of gluten-like fragments, also including the 25-mer and 33-mer-like of α-gliadin, was confirmed in beer brewed with barley and wheat malt as well as in the gluten-free beer. Both CD-toxic and allergenic peptides of all beer samples were drastically degraded when subjected to a simulated gastroduodenal (GD) digestion. After in vitro digestion, the level of gluten-like peptides assayed with the G12 competitive ELISA, was below the threshold (20 ppm) for a food to be considered as “gluten-free.” A few gliadin-derived epitopes occurred in the digests of beers crafted with wheat or Norberto-ID331 line of einkorn. In contrast, digests of all barley malt and gluten-free beers did not contain detectable gluten-like epitopes, but only minor fragments of hordeins and IgE-reactive food allergens. All beer samples evoked a weak immune response on gliadin-reactive celiac T cells isolated from intestinal biopsies of celiac patients. Compared to undigested polypeptides, the response was markedly reduced by GD digestion. Although the consumption of a moderate amount of beer brewed with barley or einkorn could deliver a relatively low amount of CD-toxic epitopes, the findings of this study emphasize the urgent need of a reliable and accurate quantification of gluten epitopes in all types of beer, also including the gluten-free one, to compute realistically the contribution of beer to the overall gluten intake, which can be responsible of intestinal tissue damages in celiacs.
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Affiliation(s)
- Valentina Spada
- Institute of Food Sciences, National Research Council (CNR), Avellino, Italy
| | - Luigia Di Stasio
- Institute of Food Sciences, National Research Council (CNR), Avellino, Italy
| | - Stefania Picascia
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Naples, Italy
| | | | - Carmen Gianfrani
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Naples, Italy
| | - Gianfranco Mamone
- Institute of Food Sciences, National Research Council (CNR), Avellino, Italy
| | - Gianluca Picariello
- Institute of Food Sciences, National Research Council (CNR), Avellino, Italy
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6
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Sun Z, Yu X, Zhang Y, Xu J, Li X. Construction of a comprehensive beer proteome map using sequential filter-aided sample preparation coupled with liquid chromatography tandem mass spectrometry. J Sep Sci 2019; 42:2835-2841. [PMID: 31218791 DOI: 10.1002/jssc.201900074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 05/07/2019] [Accepted: 06/13/2019] [Indexed: 11/10/2022]
Abstract
The quality traits of beer, which include flavor, texture, foam stability, gushing, and haze formation, rely on contributions from beer proteins and peptides. Large-scale proteomic analysis of beer is gaining importance, not only with respect to authenticity of raw material in beer but also to improve quality control during beer production. In this work, foam proteins were first isolated from beer by virtue of their high hydrophobicity. Then sequential filter-aided sample preparation coupled with liquid chromatography and tandem mass spectrometry was used to analyze both beer protein and foam protein. Finally, 4692 proteins were identified as beer proteins, and 3906 proteins were identified as foam proteins. In total, 7113 proteins were identified in the beer sample. Several proteins contributing to beer quality traits, including lipid transfer protein, serpin, hordein, gliadin, and glutenin, were detected in our proteins list. This work constructed a comprehensive beer proteome map that may help to evaluate potential health risks related to beer consumption in celiac patients.
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Affiliation(s)
- Zhen Sun
- School of Biological Engineering, Dalian Polytechnic University, Dalian, P. R. China
| | - Xinhe Yu
- School of Biological Engineering, Dalian Polytechnic University, Dalian, P. R. China
| | - Yanrong Zhang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, P. R. China
| | - Jiuxiang Xu
- School of Biological Engineering, Dalian Polytechnic University, Dalian, P. R. China
| | - Xianzhen Li
- School of Biological Engineering, Dalian Polytechnic University, Dalian, P. R. China
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7
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Neugrodda C, Gastl M, Becker T. Protein Profile Characterization of Hop (Humulus LupulusL.) Varieties. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-2014-0629-01] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Christoph Neugrodda
- Lehrstuhl für Brau- und Getränketechnologie, Technische Universität München, Weihenstephaner Steig 20, 85354 Freising, Germany
| | - Martina Gastl
- Lehrstuhl für Brau- und Getränketechnologie, Technische Universität München, Weihenstephaner Steig 20, 85354 Freising, Germany
| | - Thomas Becker
- Lehrstuhl für Brau- und Getränketechnologie, Technische Universität München, Weihenstephaner Steig 20, 85354 Freising, Germany
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8
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Grochalová M, Konečná H, Stejskal K, Potěšil D, Fridrichová D, Srbová E, Ornerová K, Zdráhal Z. Deep coverage of the beer proteome. J Proteomics 2017; 162:119-124. [DOI: 10.1016/j.jprot.2017.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/12/2017] [Accepted: 05/01/2017] [Indexed: 11/25/2022]
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9
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Schulte F, Flaschel E, Niehaus K. Proteome-Based Analysis of Colloidal Instability Enables the Detection of Haze-Active Proteins in Beer. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:6752-61. [PMID: 27515584 DOI: 10.1021/acs.jafc.6b02467] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Colloidal haze is a serious quality defect of bright beers that considerably reduces their shelf life and is thought to be triggered by hordeins, a class of proline-rich barley proteins. In this work, the proteomes of fresh and old beers were investigated in bottled pilsners and compared to the protein inventory of haze to identify specific haze-active proteins. Haze isolates dissolved in rehydration buffer contained high concentrations of proteins and sugars but provided protein gels with weak spot signals. Consequently, a treatment for the chemical deglycation with trifluoromethanesulfonic acid was applied, which resulted in the identification of protein Z4, LTP1, CMb, CMe, pUP13, 3a, and Bwiph as constituents of the haze proteome. Because only one hordein was detectable and the proline content in haze hydrolysates was lower than those of barley prolamins, our results suggest that this class of proteins is of minor importance for haze development.
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Affiliation(s)
- Fabian Schulte
- Fakultät für Biologie, Proteom- und Metabolomforschung and ‡Technische Fakultät, Fermentationstechnik, Universität Bielefeld , 33615 Bielefeld, Germany
| | - Erwin Flaschel
- Fakultät für Biologie, Proteom- und Metabolomforschung and ‡Technische Fakultät, Fermentationstechnik, Universität Bielefeld , 33615 Bielefeld, Germany
| | - Karsten Niehaus
- Fakultät für Biologie, Proteom- und Metabolomforschung and ‡Technische Fakultät, Fermentationstechnik, Universität Bielefeld , 33615 Bielefeld, Germany
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10
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Heterologous expression of Hordeum vulgare protein Z4 in Pichia pastoris shows increased structural stability. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.03.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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11
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Takahashi K, Kohno H. Different Polar Metabolites and Protein Profiles between High- and Low-Quality Japanese Ginjo Sake. PLoS One 2016; 11:e0150524. [PMID: 26939054 PMCID: PMC4777507 DOI: 10.1371/journal.pone.0150524] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 02/14/2016] [Indexed: 01/10/2023] Open
Abstract
Japanese ginjo sake is a premium refined sake characterized by a pleasant fruity apple-like flavor and a sophisticated taste. Because of technical difficulties inherent in brewing ginjo sake, off-flavors sometimes occur. However, the metabolites responsible for off-flavors as well as those present or absent in higher quality ginjo sake remain uncertain. Here, the relationship between 202 polar chemical compounds in sake identified using capillary electrophoresis coupled with time-of-flight mass spectrometry and its organoleptic properties, such as quality and off-flavor, was examined. First, we found that some off-flavored sakes contained higher total amounts of metabolites than other sake samples. The results also identified that levels of 2-oxoglutaric acid and fumaric acid, metabolites in the tricarboxylic acid cycle, were highly but oppositely correlated with ginjo sake quality. Similarly, pyridoxine and pyridoxamine, co-enzymes for amino transferase, were also highly but oppositely correlated with ginjo sake quality. Additionally, pyruvic acid levels were associated with good quality as well. Compounds involved in the methionine salvage cycle, oxidative glutathione derivatives, and amino acid catabolites were correlated with low quality. Among off-flavors, an inharmonious bitter taste appeared attributable to polyamines. Furthermore, protein analysis displayed that a diversity of protein components and yeast protein (triosephosphate isomerase, TPI) leakage was linked to the overall metabolite intensity in ginjo sake. This research provides insight into the relationship between sake components and organoleptic properties.
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Affiliation(s)
- Kei Takahashi
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-hiroshima, Hiroshima, 739–0046, Japan
- * E-mail:
| | - Hiromi Kohno
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-hiroshima, Hiroshima, 739–0046, Japan
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12
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Han Y, Wang J, Li Y, Hang Y, Yin X, Li Q. Circular dichroism and infrared spectroscopic characterization of secondary structure components of protein Z during mashing and boiling processes. Food Chem 2015; 188:201-9. [DOI: 10.1016/j.foodchem.2015.04.053] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 02/27/2015] [Accepted: 04/15/2015] [Indexed: 11/26/2022]
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13
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Picariello G, Mamone G, Cutignano A, Fontana A, Zurlo L, Addeo F, Ferranti P. Proteomics, peptidomics, and immunogenic potential of wheat beer (Weissbier). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:3579-3586. [PMID: 25793656 DOI: 10.1021/acs.jafc.5b00631] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Wheat beer is a traditional light-colored top-fermenting beer brewed with at least 50% malted (e.g., German Weissbier) or unmalted (e.g., Belgian Witbier) wheat (Triticum aestivum) as an adjunct to barley (Hordeum vulgare) malt. For the first time, we explored the proteome of three Weissbier samples, using both 2D electrophoresis (2DE)-based and 2DE-free strategies. Overall, 58 different gene products arising from barley, wheat, and yeast (Saccharomyces spp.) were identified in the protein fraction of a representative Weissbier sample analyzed in detail. Analogous to all-barley-malt beers (BMB), barley and wheat Z-type serpins and nonspecific lipid transfer proteins dominated the proteome of Weissbier. Several α-amylase/trypsin inhibitors also survived the harsh brewing conditions. During brewing, hundreds of peptides are released into beer. By liquid chromatography-electrospray tandem mass spectrometry (LC-ESI MS/MS) analysis, we characterized 167 peptides belonging to 44 proteins, including gliadins, hordeins, and high- and low-molecular-weight glutenin subunits. Because of the interference from the overabundant yeast-derived peptides, we identified only a limited number of epitopes potentially triggering celiac disease. However, Weissbier samples contained 374, 372, and 382 ppm gliadin-equivalent peptides, as determined with the competitive G12 ELISA, which is roughly 10-fold higher than a lager BMB (41 ppm), thereby confirming that Weissbier is unsuited for celiacs. Western blot analysis demonstrated that Weissbier also contained large-sized prolamins immunoresponsive to antigliadin IgA antibodies from the pooled sera of celiac patients (n = 4).
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Affiliation(s)
- Gianluca Picariello
- †Istituto di Scienze dell'Alimentazione, Consiglio Nazionale delle Ricerche, Via Roma 64, I-83100 Avellino, Italy
| | - Gianfranco Mamone
- †Istituto di Scienze dell'Alimentazione, Consiglio Nazionale delle Ricerche, Via Roma 64, I-83100 Avellino, Italy
| | - Adele Cutignano
- ‡Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, I-80078 Pozzuoli (Napoli), Italy
| | - Angelo Fontana
- ‡Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, I-80078 Pozzuoli (Napoli), Italy
| | - Lucia Zurlo
- §Dipartimento di Agraria, Università di Napoli "Federico II", Parco Gussone, I-80055 Portici (Napoli), Italy
| | - Francesco Addeo
- †Istituto di Scienze dell'Alimentazione, Consiglio Nazionale delle Ricerche, Via Roma 64, I-83100 Avellino, Italy
| | - Pasquale Ferranti
- †Istituto di Scienze dell'Alimentazione, Consiglio Nazionale delle Ricerche, Via Roma 64, I-83100 Avellino, Italy
- §Dipartimento di Agraria, Università di Napoli "Federico II", Parco Gussone, I-80055 Portici (Napoli), Italy
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14
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Purification of barley dimeric α-amylase inhibitor-1 (BDAI-1) and avenin-like protein-a (ALP) from beer and their impact on beer foam stability. Food Chem 2015; 172:257-64. [DOI: 10.1016/j.foodchem.2014.09.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 09/02/2014] [Accepted: 09/04/2014] [Indexed: 11/19/2022]
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15
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Scientific Opinion on the evaluation of allergenic foods and food ingredients for labelling purposes. EFSA J 2014. [DOI: 10.2903/j.efsa.2014.3894] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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16
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Moreda-Piñeiro A, García-Otero N, Bermejo-Barrera P. A review on preparative and semi-preparative offgel electrophoresis for multidimensional protein/peptide assessment. Anal Chim Acta 2014; 836:1-17. [PMID: 24974865 DOI: 10.1016/j.aca.2014.04.053] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 04/23/2014] [Accepted: 04/27/2014] [Indexed: 11/29/2022]
Abstract
Mass spectrometry (MS) techniques are commonly used for protein identification and further analysis of selected protein spots after high resolution 2-D electrophoresis. Complementary gel-free approaches have been developed during the last few years and have shown to be useful tools in modern proteomics. The development and application of various gel-free electrophoresis devices for performing protein fractionation according to the pI differences is therefore a topic of interest. This review describes the current state of isoelectric focusing (IEF) gel-free electrophoresis based on the Agilent offgel 3100 fractionator. The review includes, therefore, (i) an overview on IEF as well as other previous IEF gel-free electrophoresis developments; (ii) offgel fundamentals and future trends; (iii) advantages and disadvantages of current offgel procedures; (iv) requirements of isolated protein pellets for further offgel fractionation; (v) offgel fraction requirements to perform the second dimensional analysis by advance electrophoresis and chromatographic techniques; and (vi) effect of the offgel operating conditions on the stability of metal-protein complexes.
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Affiliation(s)
- Antonio Moreda-Piñeiro
- Department of Analytical Chemistry, Nutrition and Bromatology, Faculty of Chemistry, University of Santiago de Compostela, Avenida das Ciencias, s/n. 15782 Santiago de Compostela, Spain.
| | - Natalia García-Otero
- Department of Analytical Chemistry, Nutrition and Bromatology, Faculty of Chemistry, University of Santiago de Compostela, Avenida das Ciencias, s/n. 15782 Santiago de Compostela, Spain
| | - Pilar Bermejo-Barrera
- Department of Analytical Chemistry, Nutrition and Bromatology, Faculty of Chemistry, University of Santiago de Compostela, Avenida das Ciencias, s/n. 15782 Santiago de Compostela, Spain
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17
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Dedvisitsakul P, Jacobsen S, Svensson B, Bunkenborg J, Finnie C, Hägglund P. Glycopeptide Enrichment Using a Combination of ZIC-HILIC and Cotton Wool for Exploring the Glycoproteome of Wheat Flour Albumins. J Proteome Res 2014; 13:2696-703. [DOI: 10.1021/pr401282r] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Plaipol Dedvisitsakul
- Enzyme
and Protein Chemistry, Søltofts Plads Building 224, Department
of Systems Biology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Susanne Jacobsen
- Enzyme
and Protein Chemistry, Søltofts Plads Building 224, Department
of Systems Biology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Birte Svensson
- Enzyme
and Protein Chemistry, Søltofts Plads Building 224, Department
of Systems Biology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Jakob Bunkenborg
- Department
of Clinical Biochemistry, Copenhagen University Hospital Hvidovre, DK-2650 Hvidovre, Denmark
- Center
of Experimental BioInformatics, Department of Biochemistry and Molecular
Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
| | - Christine Finnie
- Agricultural
and Environmental Proteomics, Søltofts Plads Building 224, Department
of Systems Biology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Per Hägglund
- Enzyme
and Protein Chemistry, Søltofts Plads Building 224, Department
of Systems Biology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
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18
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Magdeldin S, Yamamoto K, Yoshida Y, Xu B, Zhang Y, Fujinaka H, Yaoita E, Yates JR, Yamamoto T. Deep proteome mapping of mouse kidney based on OFFGel prefractionation reveals remarkable protein post- translational modifications. J Proteome Res 2014; 13:1636-46. [PMID: 24495006 PMCID: PMC3993965 DOI: 10.1021/pr401122m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
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Performing a comprehensive
nonbiased proteome analysis is an extraordinary
challenge due to sample complexity and wide dynamic range, especially
in eukaryotic tissues. Thus, prefractionation steps conducted prior
to mass spectrometric analysis are critically important to reduce
complex biological matrices and allow in-depth analysis. Here we demonstrated
the use of OFFGel prefractionation to identify more low abundant and
hydrophobic proteins than in a nonfractionated sample. Moreover, OFFGel
prefractionation of a kidney protein sample was able to unveil protein
functional relevance by detecting PTMs, especially when prefractionation
was augmented with a targeted enrichment strategy such as TiO2 phospho-enrichment. The OFFGel-TiO2 combination
used in this study was comparable to other global phosphoproteomics
approaches (SCX-TiO2, ERLIC-TiO2, or HILIC-TiO2). The detailed mouse kidney proteome with the phosphopeptide
enrichment presented here serves as a useful platform for a better
understanding of how the renal protein modification machinery works
and, ultimately, will contribute to our understanding of pathological
processes as well as normal physiological renal functions.
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Affiliation(s)
- Sameh Magdeldin
- Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University , Niigata, Japan
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Abstract
Proteome analysis provides a way to identify proteins related to the quality traits of beer. A number of protein species in beer and wort have been identified by two-dimensional gel electrophoresis combined with enzyme digestion such as trypsin, followed by mass spectrometry analyses and/or liquid chromatography mass/mass spectrometry. In addition, low molecular weight polypeptides in beer have been identified by the combination of non-enzyme digestion and mass analyses. These data sets of various molecular weight polypeptides (i.e., proteomes) provide a platform for analyzing protein functions in beer. Several novel proteins related to beer quality traits such as foam stability and haze formation have been identified by analyzing these proteomes. Some of the proteins have been applied to the development of efficient protein or DNA markers for trait selection in malting barley breeding. In this chapter, recent proteome studies of beer and wort are reviewed, and the methods and protocols of beer and wort proteome analysis are described.
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Affiliation(s)
- Takashi Iimure
- Bioresources Research and Development Department, Sapporo Breweries Ltd., Ota, Gunma, Japan
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Iimure T, Sato K. Beer proteomics analysis for beer quality control and malting barley breeding. Food Res Int 2013. [DOI: 10.1016/j.foodres.2012.11.028] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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21
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Colgrave ML, Goswami H, Howitt CA, Tanner GJ. Proteomics as a tool to understand the complexity of beer. Food Res Int 2013. [DOI: 10.1016/j.foodres.2012.09.043] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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22
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Berner TS, Jacobsen S, Arneborg N. The impact of different ale brewer's yeast strains on the proteome of immature beer. BMC Microbiol 2013; 13:215. [PMID: 24079909 PMCID: PMC3849757 DOI: 10.1186/1471-2180-13-215] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 09/23/2013] [Indexed: 11/16/2022] Open
Abstract
Background It is well known that brewer’s yeast affects the taste and aroma of beer. However, the influence of brewer’s yeast on the protein composition of beer is currently unknown. In this study, changes of the proteome of immature beer, i.e. beer that has not been matured after fermentation, by ale brewer’s yeast strains with different abilities to degrade fermentable sugars were investigated. Results Beers were fermented from standard hopped wort (13° Plato) using two ale brewer’s yeast (Saccharomyces cerevisiae) strains with different attenuation degrees. Both immature beers had the same alcohol and protein concentrations. Immature beer and unfermented wort proteins were analysed by 2-DE and compared in order to determine protein changes arising from fermentation. Distinct protein spots in the beer and wort proteomes were identified using Matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and MS/MS and revealed common beer proteins, such as lipid transfer proteins (LTP1 and LTP2), protein Z and amylase-protease inhibitors. During fermentation, two protein spots, corresponding to LTP2, disappeared, while three protein spots were exclusively found in beer. These three proteins, all derived from yeast, were identified as cell wall associated proteins, that is Exg1 (an exo-β-1,3-glucanase), Bgl2 (an endo-β-1,2-glucanase), and Uth1 (a cell wall biogenesis protein). Conclusion Yeast strain dependent changes in the immature beer proteome were identified, i.e. Bgl2 was present in beer brewed with KVL011, while lacking in WLP001 beer.
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Affiliation(s)
- Torben Sune Berner
- Food Microbiology, Department of Food Science, University of Copenhagen, DK-1958, Frederiksberg, Denmark.
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Šedo O, Márová I, Zdráhal Z. Beer fingerprinting by Matrix-Assisted Laser Desorption-Ionisation-Time of Flight Mass Spectrometry. Food Chem 2012; 135:473-8. [DOI: 10.1016/j.foodchem.2012.05.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 04/27/2012] [Accepted: 05/02/2012] [Indexed: 10/28/2022]
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Shotgun proteome analysis of beer and the immunogenic potential of beer polypeptides. J Proteomics 2012; 75:5872-82. [PMID: 22868252 DOI: 10.1016/j.jprot.2012.07.038] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 07/16/2012] [Accepted: 07/22/2012] [Indexed: 01/05/2023]
Abstract
The majority of beer proteins originate from barley (Hordeum vulgare) which is used for brewing. Barley is known to contain celiacogenic gliadin-like prolamins (hordeins) along with other immunogenic proteins which endure malt proteases and the harsh conditions of brewing. In addition, a multitude of peptides that may retain or even amplify the immune-stimulating potential is released in beer because of proteolysis. The comprehensive annotation of the beer proteome is challenged both by the high concentration range of the protein entities and by a severe degree of processing-induced modifications. Overcoming the pitfalls of the classical two-dimensional electrophoresis approach coupled to mass spectrometry (MS), the gel-free shotgun proteomic analysis expanded the current inventory of a popular Italian beer to 33 gene products, including traces of intact B- and D-hordeins and 10 proteins from Saccharomyces spp. The high performance liquid chromatography-electrospray MS/MS peptidomic analysis of the low-molecular weight beer components disclosed a panel of hordein-derived peptides that encrypt gluten-like sequence motifs, potentially harmful to celiacs. The presence of antigliadin IgA-immunoresponsive prolamins was assayed by Western and dot blot using sera of N=4 celiac patients. Gliadin-reactive T-cell lines isolated from the intestine of N=5 celiacs activated an IFN-γ response when challenged with deamidated beer polypeptides.
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