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Boschetti E, Zilberstein G, Righetti PG. Combinatorial peptides: A library that continuously probes low-abundance proteins. Electrophoresis 2021; 43:355-369. [PMID: 34498305 DOI: 10.1002/elps.202100131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/31/2021] [Accepted: 08/24/2021] [Indexed: 12/12/2022]
Abstract
After a decade of experimental applications, it is the objective of this review to make a point on combinatorial peptide ligand libraries dedicated to low-abundance proteins from animals to plants and to microorganism proteomics. It is, thus, at the light of the recent technical developments and applications that we will examine the state of the art, its usage within the scientific community, and its openness to unexplored fields. The improvements of the methodology and its implementation in connection with analytical determinations of combinatorial peptide ligand library (CPLL)-treated samples are extensively reviewed and commented upon. Relevant examples covering few critical aspects describe the performance of the technology. Finally, a reflection on the technological future is attempted in particular by involving new concepts adapted to the limited availability of certain biological samples.
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Affiliation(s)
| | | | - Pier Giorgio Righetti
- Department of Chemistry Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milan, Italy
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The Role of Enolases in Allergic Disease. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE 2021; 9:3026-3032. [PMID: 33862268 DOI: 10.1016/j.jaip.2021.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/03/2021] [Accepted: 04/05/2021] [Indexed: 12/13/2022]
Abstract
Enolase is one of the most abundant cytosolic enzymes as well as an important glycolytic metalloenzyme highly conserved among organisms from different taxonomical groups. Participation of enolase in processes in which its enzymatic activity is not required has been widely reported. Some of these processes provide special qualities to microorganisms, which favor, in some cases, their pathogenicity. Remarkably, enolase has been reported as an allergen by itself, it is well recognized as allergenic in molds and yeasts, whereas it has also been recognized by the immune system of susceptible individuals acting as a food and inhaled allergen from other diverse sources such as insects, birds, fishes, and plants. To date, 14 enolases have been officially recognized by the World Health Organization/International Union of Immunological Societies Allergen Nomenclature Subcommittee. The use of discovery proteomics has also uncovered novel allergenic enolases, particularly from pollen sources. Here, we review the relevance of enolases as sensitizers and as nonsensitizing cross-reactive allergens in allergic disease.
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Insight of low-abundance proteins in rice leaves under Cd stress using combinatorial peptide ligand library technology. Anal Bioanal Chem 2020; 412:5435-5446. [DOI: 10.1007/s00216-020-02760-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/18/2020] [Accepted: 06/05/2020] [Indexed: 01/22/2023]
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He Y, Song Q, Wu Y, Ye S, Chen S, Chen H. TMT-Based Quantitative Proteomic Analysis Reveals the Crucial Biological Pathways Involved in Self-Incompatibility Responses in Camellia oleifera. Int J Mol Sci 2020; 21:ijms21061987. [PMID: 32183315 PMCID: PMC7139391 DOI: 10.3390/ijms21061987] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/09/2020] [Accepted: 03/12/2020] [Indexed: 12/25/2022] Open
Abstract
Camellia oleifera is a valuable woody oil plant belonging to the Theaceae, Camellia oil extracted from the seed is an excellent edible oil source. Self-incompatibility (SI) in C. oleifera results in low fruit set, and our knowledge about the mechanism remains limited. In the present study, the Tandem mass tag (TMT) based quantitative proteomics was employed to analyze the dynamic change of proteins response to self- and cross-pollinated in C. oleifera. A total of 6,616 quantified proteins were detected, and differentially abundant proteins (DAPs) analysis identified a large number of proteins. Combined analysis of differentially expressed genes (DEGs) and DAPs of self- and cross-pollinated pistils based on transcriptome and proteome data revealed that several candidate genes or proteins involved in SI of C. oleifera, including polygalacturonase inhibitor, UDP-glycosyltransferase 92A1-like, beta-D-galactosidase, S-adenosylmethionine synthetase, xyloglucan endotransglucosylase/hydrolase, ABC transporter G family member 36-like, and flavonol synthase. Venn diagram analysis identified 11 proteins that may participate in pollen tube growth in C. oleifera. Our data also revealed that the abundance of proteins related to peroxisome was altered in responses to SI in C. oleifera. Moreover, the pathway of lipid metabolism-related, flavonoid biosynthesis and splicesome were reduced in self-pollinated pistils by the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. In summary, the results of the present study lay the foundation for learning the regulatory mechanism underlying SI responses as well as provides valuable protein resources for the construction of self-compatibility C. oleifera through genetic engineering in the future.
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Affiliation(s)
- Yifan He
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; (Y.H.); (Q.S.); (Y.W.); (S.Y.); (S.C.)
- Forestry College, Oil Tea Research Center of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Qianqian Song
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; (Y.H.); (Q.S.); (Y.W.); (S.Y.); (S.C.)
- Forestry College, Oil Tea Research Center of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Yuefeng Wu
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; (Y.H.); (Q.S.); (Y.W.); (S.Y.); (S.C.)
- Forestry College, Oil Tea Research Center of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Shutao Ye
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; (Y.H.); (Q.S.); (Y.W.); (S.Y.); (S.C.)
- Forestry College, Oil Tea Research Center of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Shipin Chen
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; (Y.H.); (Q.S.); (Y.W.); (S.Y.); (S.C.)
- Forestry College, Oil Tea Research Center of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Hui Chen
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; (Y.H.); (Q.S.); (Y.W.); (S.Y.); (S.C.)
- Forestry College, Oil Tea Research Center of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- Correspondence: ; Tel.: +86-139-5034-3791
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Righetti PG, Boschetti E. Low-abundance plant protein enrichment with peptide libraries to enlarge proteome coverage and related applications. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 290:110302. [PMID: 31779915 DOI: 10.1016/j.plantsci.2019.110302] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/15/2019] [Accepted: 10/05/2019] [Indexed: 06/10/2023]
Abstract
In plant tissues proteins are present in low amounts but in a very large number. To this peculiar situation many complex foreign components render protein extraction and purification very difficult. In the last several years interesting technologies have been described to improve the technical situation to the point that some methodologies allow reaching very low-abundance proteins and minor allergens. Among enrichment methods the one documented in this report is based on combinatorial peptide ligand libraries (CPLLs) that emerged in the last decade by contributing to largely improve the knowledge in plant proteomics. It is the aim of this review to describe how this technology allows detecting low-abundance proteins from various plant tissues and to report the dynamics of the proteome components in response to environmental changes and biotic attacks. Typical documented examples with the description of their scientific interest are reported. The described technical approach and selected applications are considered as one of the most advanced approaches for plant proteomics investigations with possibilities not only to enlarge the knowledge of plant proteomes but also to discover novel allergens as well as plant biomarkers subsequent to stressful situations.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Chemistry Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, 20131, Milan, Italy.
| | - Egisto Boschetti
- Scientific Consultant, JAM Conseil, 92200, Neuilly-sur-Seine, France
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Shahali Y, Sénéchal H, Poncet P. The Use of Combinatorial Hexapeptide Ligand Library (CPLL) in Allergomics. Methods Mol Biol 2019; 1871:393-403. [PMID: 30276749 DOI: 10.1007/978-1-4939-8814-3_21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
The recent progress of proteomic protocols led to more efficient protein extraction and concentration procedures to remove nonprotein interfering compounds present in the starting material and to increase the concentration of underrepresented proteins. Combinatorial hexapeptide ligand libraries (CPLL) were recently applied to both plant- and animal-derived tissues for capturing the low- and very low-abundance allergens. Several IgE-binding proteins which were previously absent or poorly represented by using conventional proteomics tools have been detected and characterized through a CPLL-based approach. In the present chapter, a protocol based on improved protein extraction and enrichment by CPLL, allowing the immunochemical characterization of several "hidden allergens" in cypress pollen, is described in detail.
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Affiliation(s)
- Youcef Shahali
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension organization (AREEO), Karaj, Iran.
| | - Hélène Sénéchal
- Armand Trousseau Children Hospital, AP-HP, Biochemistry Department, Allergy and Environment Team, Paris, France
| | - Pascal Poncet
- Armand Trousseau Children Hospital, AP-HP, Biochemistry Department, Allergy and Environment Team, Paris, France
- Institut Pasteur, Center for Innovation and Technological Research, Paris, France
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Double One-Dimensional Electrophoresis (D1-DE) Adapted for Immunoproteomics. Methods Mol Biol 2018. [PMID: 30276737 DOI: 10.1007/978-1-4939-8814-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The classical proteomics approach for the identification of allergen candidates consists on the separation of proteins by high-resolution two-dimensional electrophoresis (2-DE) with subsequent IgE immunoblotting and further analysis of IgE-reactive protein spots with mass spectrometry. In this approach at least two gels most be run. One gel is used for staining and the other is for immunoblotting by antibodies labeled with specific immunostains. Additional functional characterizations require either protein purification or 2-DE replicates and appear to be time- and reagent-consuming. Here we described a modified double one-dimensional electrophoresis (D1-DE) allowing the conversion of a protein spot previously visualized by 2-DE into an extended protein band. In D1-DE, the purity of the protein of interest is similar to 2-DE spots, but its abundance is many times higher than what can be found in a 2-DE single spot allowing many other functional analyses from a single D1-DE separation.
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Novel low-abundance allergens from mango via combinatorial peptide libraries treatment: A proteomics study. Food Chem 2018; 269:652-660. [PMID: 30100485 DOI: 10.1016/j.foodchem.2018.06.113] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/22/2018] [Accepted: 06/21/2018] [Indexed: 11/24/2022]
Abstract
Mango allergy is a rare condition, which may cause severe hypersensitivity reactions, such as anaphylaxis, angioedema, asthma and contact dermatitis. By exploiting the combinatorial peptide ligand library (CPLL) technology, mango proteomes have been extracted and the presence of traces of allergens assessed via Western blot analysis two-dimensional maps. Upon reactive spot elution and mass spectrometry analyses, four major mango allergens could be identified for the first time and shown to be in common with three of the five known banana species. These allergens include: Mus a 1, Mus a 2 and Mus a 5. Additional mango allergens detected do not seem to be in common with the banana species. In particular, a pectinesterase and a superoxide dismutase, both widely described as allergens, could be identified in mango extracts. Conversely, plain mango extracts not treated with CPLLs did not exhibit any reactive spots in Western blot analysis.
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Mousavi F, Majd A, Shahali Y, Ghahremaninejad F, Shokouhi Shoormasti R, Pourpak Z. Immunoproteomics of tree of heaven (Ailanthus atltissima) pollen allergens. J Proteomics 2016; 154:94-101. [PMID: 28041857 DOI: 10.1016/j.jprot.2016.12.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 11/30/2016] [Accepted: 12/19/2016] [Indexed: 12/12/2022]
Abstract
Ailanthus altissima pollen (AAP) is considered as an emerging cause of respiratory allergy in United States, Italy and Iran. However, the allergenic composition of AAP is still unknown and has yet to be characterized. The present study aimed to identify AAP allergens using a proteomics-based approach. For this purpose, optimized AAP protein extracts were analyzed using 1D- and 2D- gel electrophoresis and confronted to twenty sera from individuals with respiratory allergy during the AAP season. Candidate allergens were detected using the serum from an allergic patient with clinical history of AAP pollinosis. IgE-binding spots were identified using MALDI-TOF/TOF mass spectrometry and database searching. According to our results, AAP extracts were rich in proteins (up to 16.25mg/ml) with a molecular-weight distribution ranging from 10 to 175kDa. Two-D electrophoresis of AAP extracts revealed 125 protein spots from which 13 were IgE reactive. These IgE-binding proteins were identified as enolase, calreticulin, probable pectate lyase 6, conserved hypothetical protein and ras-related protein RHN1-like. By our knowledge, this study is the first report identifying AAP allergens. These findings will open up further avenues for the diagnosis and immunotherapy of the AAP allergy as well as for the cloning and molecular characterization of relevant allergens. BIOLOGICAL SIGNIFICANCE Ailanthus altissima colonizes new areas every year in Iran and is spreading aggressively worldwide. According to USDA, the tree of heaven is now present as an invasive plant in 30 states in US (www.invasivespeciesinfo.gov/plants/treeheaven.shtml) and come to dominate large areas in many regions. Up to now, several cases of allergy to A. altissima pollen have been reported in United States, Italy and Iran [1-4]. However, there is still no information on the sensitizing allergens and the molecular origin of these clinical symptoms, which constitutes a serious threat to patients suffering from respiratory allergies in these regions. To our knowledge, the current study describes, therefore, the first panel of proteins responsible for IgE-mediated A. altissima pollinosis by using a gel-based proteomic approach. This work represents the pioneer proteomic investigation on Simaroubaceae spp. and provides useful insights for further studies on the allergens of this widely distributed plant family.
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Affiliation(s)
- Fateme Mousavi
- Department of Plant Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Ahmad Majd
- Department of Plant Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran; Department of Biology, Faculty of Biological Sciences, Islamic Azad University, North Tehran Branch, Tehran, Iran
| | - Youcef Shahali
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
| | - Farrokh Ghahremaninejad
- Department of Plant Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | | | - Zahra Pourpak
- Immunology, Asthma and Allergy Research Institute, Tehran University of Medical Sciences, Tehran, Iran
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Global proteome analysis in plants by means of peptide libraries and applications. J Proteomics 2016; 143:3-14. [DOI: 10.1016/j.jprot.2016.02.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 02/20/2016] [Accepted: 02/26/2016] [Indexed: 01/07/2023]
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Hyphenated LC-MALDI-ToF/ToF and LC-ESI-QToF approach in proteomic characterization of honeybee venom. J Pharm Biomed Anal 2016; 121:69-76. [PMID: 26780156 DOI: 10.1016/j.jpba.2016.01.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/17/2015] [Accepted: 01/02/2016] [Indexed: 01/31/2023]
Abstract
To increase in the depth characterization of venom proteome of Apis mellifera the hyphenated LC-MALDI-ToF/ToF-MS (liquid chromatography-matrix-assisted laser desorption/ionization-time of flight/time of flight tandem mass spectrometry) and LC-ESI-QToF-MS (liquid chromatography-electrospray ionization-quadrupole time of flight tandem mass spectrometry) techniques combined with combinatorial peptide ligand library enrichment method is proposed in this study. The novel approach simplifies pretreatment protocol in venom investigation. By using the protein preparation kit with sequential multi-step elution, the honeybee venom was dispensed into four different fractions. In total 269 proteins were detected, among these 49 honeybee toxins, allergens and components involved in mechanism of envenoming belonging to venom enzyme classes of esterases, proteases/peptidases, protease inhibitors, hydrolases and major royal jelly proteins. Moreover 5 additional putative toxins were identified. Their role in envenoming process was discussed. We concluded that different mass spectrometry techniques increased the detection of the honeybee venom proteins, underscoring the complementary character of analytical methods. The combination of MALDI and ESI ionization has resulted in numerous proteins identifications, not possible to reach with single proteomic technique. The study will contribute to broadening the knowledge about the complexity of honeybee venom. The newly identified proteins may serve not only as toxins and allergens, but also as substances with potential pharmacological activity. Although, the most detected proteins belong to trace elements of honeybee venom without toxic activity or action on vital system of victims, they should be taken into account in characterization of living organism response on Apis mellifera sting.
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Sénéchal H, Visez N, Charpin D, Shahali Y, Peltre G, Biolley JP, Lhuissier F, Couderc R, Yamada O, Malrat-Domenge A, Pham-Thi N, Poncet P, Sutra JP. A Review of the Effects of Major Atmospheric Pollutants on Pollen Grains, Pollen Content, and Allergenicity. ScientificWorldJournal 2015; 2015:940243. [PMID: 26819967 PMCID: PMC4706970 DOI: 10.1155/2015/940243] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 10/30/2015] [Accepted: 11/09/2015] [Indexed: 12/12/2022] Open
Abstract
This review summarizes the available data related to the effects of air pollution on pollen grains from different plant species. Several studies carried out either on in situ harvested pollen or on pollen exposed in different places more or less polluted are presented and discussed. The different experimental procedures used to monitor the impact of pollution on pollen grains and on various produced external or internal subparticles are listed. Physicochemical and biological effects of artificial pollution (gaseous and particulate) on pollen from different plants, in different laboratory conditions, are considered. The effects of polluted pollen grains, subparticles, and derived aeroallergens in animal models, in in vitro cell culture, on healthy human and allergic patients are described. Combined effects of atmospheric pollutants and pollen grains-derived biological material on allergic population are specifically discussed. Within the notion of "polluen," some methodological biases are underlined and research tracks in this field are proposed.
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Affiliation(s)
- Hélène Sénéchal
- Allergy & Environment Team, Biochemistry Department, Armand Trousseau Children Hospital (AP-HP), 26 avenue du Dr. Arnold Netter, 75571 Paris, France
| | - Nicolas Visez
- Physical Chemistry of Combustion and Atmosphere Processes (PC2A), UMR CNRS 8522, University of Lille, 59655 Villeneuve d'Ascq, France
| | - Denis Charpin
- Pneumo-Allergology Department, North Hospital, 265 chemin des Bourrely, 13915 Marseille 20, France
| | - Youcef Shahali
- Allergy & Environment Team, Biochemistry Department, Armand Trousseau Children Hospital (AP-HP), 26 avenue du Dr. Arnold Netter, 75571 Paris, France
- Persiflore, 18 avenue du Parc, 91220 Le Plessis-Pâté, France
| | | | - Jean-Philippe Biolley
- SEVE Team, Ecology and Biology of Interactions (EBI), UMR-CNRS-UP 7267, University of Poitiers, 3 rue Jacques Fort, 86073 Poitiers, France
| | | | - Rémy Couderc
- Biochemistry Department, Armand Trousseau Children Hospital (AP-HP), 26 avenue du Dr. Arnold Netter, 75571 Paris 12, France
| | - Ohri Yamada
- French Agency for Food, Environmental and Occupational Health Safety, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort, France
| | - Audrey Malrat-Domenge
- French Agency for Food, Environmental and Occupational Health Safety, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort, France
| | - Nhân Pham-Thi
- Allergology Department, Pasteur Institute, 25-28 rue du Dr. Roux, 75724 Paris 15, France
| | - Pascal Poncet
- Allergy & Environment Team, Biochemistry Department, Armand Trousseau Children Hospital (AP-HP), 26 avenue du Dr. Arnold Netter, 75571 Paris, France
- Infections & Epidemiology Department, Pasteur Institute, 25-28 rue du Dr. Roux, 75724 Paris 15, France
| | - Jean-Pierre Sutra
- Allergy & Environment Team, Biochemistry Department, Armand Trousseau Children Hospital (AP-HP), 26 avenue du Dr. Arnold Netter, 75571 Paris, France
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Castro L, Crespo JF, Rodríguez J, Rodríguez R, Villalba M. Immunoproteomic tools are used to identify masked allergens: Ole e 12, an allergenic isoflavone reductase from olive (Olea europaea) pollen. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1871-1880. [DOI: 10.1016/j.bbapap.2015.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 09/11/2015] [Accepted: 09/17/2015] [Indexed: 01/21/2023]
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Righetti PG, Boschetti E. Sample treatment methods involving combinatorial peptide ligand libraries for improved proteomes analyses. Methods Mol Biol 2015; 1243:55-82. [PMID: 25384740 DOI: 10.1007/978-1-4939-1872-0_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
If used in an optimized manner, the technology of combinatorial peptide solid-phase libraries can easily improve the analytical determinations of proteomes by several factors. The discovery of novel species and of early stage biomarkers becomes thus reachable with a simple sample treatment. This report describes the most important point to consider (overloading and full recovery) along with a minimum scientific background and gives then detailed recipes to laboratory technicians. Orientations for optional routes are also given according to the objective of the experimental investigations. This covers different approaches to capture proteins of very low abundance. Total protein harvestings to prevent partial losses are also described such as single exhaustive desorption and fractionated elutions for more detailed analyses. Documented results are also reported demonstrating the capability of the technology well beyond what is the common assumption.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Mancinelli 7, Milan, 20131, Italy
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Righetti PG, Candiano G, Citterio A, Boschetti E. Combinatorial Peptide Ligand Libraries as a “Trojan Horse” in Deep Discovery Proteomics. Anal Chem 2014; 87:293-305. [DOI: 10.1021/ac502171b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Pier Giorgio Righetti
- Politecnico di Milano, Department of Chemistry, Materials and Chemical Engineering “Giulio
Natta”, Via Mancinelli
7, Milano 20131, Italy
| | - Giovanni Candiano
- Laboratory on Pathophysiology of Uremia
and Department of Nephrology, Istituto Giannina Gaslini, Genova, Italy
| | - Attilio Citterio
- Politecnico di Milano, Department of Chemistry, Materials and Chemical Engineering “Giulio
Natta”, Via Mancinelli
7, Milano 20131, Italy
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Abstract
The question of low-abundance proteins from biological tissues is still a major issue. Technologies have been devised to improve the situation and in the last few years a method based on solid-phase combinatorial peptide ligand libraries has been extensively applied to animal extracts. This method has also been extended to plant extracts taking advantage of findings from previous experience. Detailed methods are described and their pertinence highlighted according to various situations of plant sample origin, size of the sample, and analytical methods intended to be used for protein identifications.
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Making Progress in Plant Proteomics for Improved Food Safety. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/b978-0-444-62650-9.00006-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Ciardiello MA, Tamburrini M, Liso M, Crescenzo R, Rafaiani C, Mari A. Food allergen profiling: A big challenge. Food Res Int 2013. [DOI: 10.1016/j.foodres.2013.03.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Combinatorial peptide libraries to overcome the classical affinity-enrichment methods in proteomics. Amino Acids 2013; 45:219-29. [DOI: 10.1007/s00726-013-1505-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 04/20/2013] [Indexed: 12/11/2022]
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