Proteomics-Based Methodologies for the Detection and Quantification of Seafood Allergens

Burks, 2012, ICON: Food allergy, J. Allergy Clin. Immunol., 129, 906, 10.1016/j.jaci.2012.02.001

Sicherer, 2018, Food allergy: A review and update on epidemiology, pathogenesis, diagnosis, prevention, and management, J. Allergy Clin. Immunol., 141, 41, 10.1016/j.jaci.2017.11.003

Matricardi, 2016, EAACI Molecular Allergology User’s Guide, Pediatr. Allergy Immunol., 23, 1, 10.1111/pai.12563

EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA) (2014). Scientific Opinion on the evaluation of allergenic foods and food ingredients for labelling purposes. EFSA J., 12, 3894.

Ruethers, 2018, Seafood allergy: A comprehensive review of fish and shellfish allergens, Mol. Immunol., 100, 28, 10.1016/j.molimm.2018.04.008

Jeebhay, 2019, Food processing and occupational respiratory allergy—An EAACI position paper, Allergy, 74, 1852, 10.1111/all.13807

Pandey, 2000, Proteomics to study genes and genomes, Nature, 405, 837, 10.1038/35015709

Rabilloud, 2011, Two-dimensional gel electrophoresis in proteomics: A tutorial, J. Proteom., 74, 1829, 10.1016/j.jprot.2011.05.040

Carrera, 2007, De novo mass spectrometry sequencing and characterization of species-specific peptides from nucleoside diphosphate kinase B for the classification of commercial fish species belonging to the family Merlucciidae, J. Proteome Res., 6, 3070, 10.1021/pr0701963

Mayer, 2015, Targeted analysis of protein phosphorylation by 2D electrophoresis, Methods Mol. Biol., 1306, 167, 10.1007/978-1-4939-2648-0_13

Pazos, 2011, Fish proteins as targets of ferrous-catalyzed oxidation: Identification of protein carbonyls by fluorescent labeling on two-dimensional gels and MALDI-TOF/TOF mass spectrometry, J. Agric. Food Chem., 59, 7962, 10.1021/jf201080t

Geng, 2015, Mass spectrometry and two-dimensional electrophoresis to characterize the glycosylation of hen egg white ovomacroglobulin, J. Agric. Food Chem., 63, 8209, 10.1021/acs.jafc.5b02618

Martinotti, 2016, 2-DE Gel Analysis: The spot detection, Methods Mol. Biol., 1384, 155, 10.1007/978-1-4939-3255-9_9

Zhang, 2013, Protein analysis by shotgun/bottom-up proteomics, Chem. Rev., 113, 2343, 10.1021/cr3003533

Wolters, 2001, An automated multidimensional protein identification technology for shotgun proteomics, Anal. Chem., 73, 5683, 10.1021/ac010617e

Perkins, 1999, Probability-based protein identification by searching sequence databases using mass spectrometry data, Electrophoresis, 20, 3551, 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2

Eng, 1994, An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database, J. Am. Soc. Mass Spectrom., 5, 976, 10.1016/1044-0305(94)80016-2

Craig, 2004, TANDEM: Matching proteins with tandem mass spectra, Bioinformatics, 20, 1466, 10.1093/bioinformatics/bth092

Kall, 2007, Semi-supervised learning for peptide identification from shotgun proteomics datasets, Nat. Methods, 4, 923, 10.1038/nmeth1113

Keller, 2002, Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search, Anal. Chem., 74, 5383, 10.1021/ac025747h

Shevchenko, 1997, Peptide sequencing by mass spectrometry for homology searches and cloning of genes, J. Protein Chem., 16, 481, 10.1023/A:1026361427575

Ma, 2003, PEAKS: Powerful software for peptide de novo sequencing by tandem mass spectrometry, Rapid Commun. Mass Spectrom., 17, 2337, 10.1002/rcm.1196

Scigelova, M., Maroto, F., Dufresne, C., and Vázquez, J. (2007, June 12). High Throughput de Novo Sequencing. Available online: http://www.thermo.com/.

Bern, M., Kil, Y.J., and Becker, C. (2012). Byonic: Advanced peptide and protein identification software. Curr. Protoc. Bioinf.

Mateos, 2015, iTRAQ-based analysis of progerin expression reveals mitochondrial dysfunction, reactive oxygen species accumulation and altered proteostasis, Stem Cell Res. Ther., 6, 119, 10.1186/s13287-015-0110-5

Robotti, 2018, 2D-DIGE and fluorescence image analysis, Methods Mol. Biol., 1664, 25, 10.1007/978-1-4939-7268-5_3

Mateos, 2019, Proteome profiling of L3 and L4 Anisakis simplex development stages by TMT-based quantitative proteomics, J. Proteom., 201, 1, 10.1016/j.jprot.2019.04.006

2006, Quantitative proteomics using 16O/18O labeling and linear ion trap mass spectrometry, Proteomics, 6, S4, 10.1002/pmic.200500375

Ong, 2002, Stable isotope labelling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics, Mol. Cell. Proteom., 1, 376, 10.1074/mcp.M200025-MCP200

Mueller, 2007, SuperHirn—A novel tool for high resolution LC-MS-based peptide/protein profiling, Proteomics, 7, 3470, 10.1002/pmic.200700057

Carrera, 2017, Fast global phosphoproteome profiling of Jurkat T cells by HIFU-TiO2-SCX-LC-MS/MS, Anal. Chem., 89, 8853, 10.1021/acs.analchem.7b01321

Nilsson, 2016, Liquid chromatography-tandem mass spectrometry-based fragmentation analysis of glycopeptides, Glycoconj. J., 33, 261, 10.1007/s10719-016-9649-3

Diallo, 2019, Current trends in protein acetylation analysis, Expert Rev. Proteom., 16, 139, 10.1080/14789450.2019.1559061

Fornelli, 2018, Top-down proteomics: Where we are, where we are going?, J. Proteom., 175, 3, 10.1016/j.jprot.2017.02.002

Carrera, 2010, Extensive de novo sequencing of new parvalbumin isoforms using a novel combination of bottom-up proteomics, accurate molecular mass measurement by FTICR-MS, and selected MS/MS ion monitoring, J. Proteome Res., 9, 4393, 10.1021/pr100163e

Carrera, M., Weisbrod, C., Lopez-Ferrer, D., Huguet, R., Gallardo, J.M., Schwartz, J., and Huhmer, A. (2015). Top-Down, High throughput of Thermo-Stable Allergens Using Complementary MS/MS Fragmentation Strategies, Thermo Fisher Scientific. PN64488-EN 0615S.

2017, What is targeted proteomics? A concise revision of targeted acquisition and targeted data analysis in mass spectrometry, Proteomics, 17, 17

Aebersold, 2016, Applications and developments in targeted proteomics: From SRM to DIA/SWATH, Proteomics, 16, 2065, 10.1002/pmic.201600203

Lange, 2008, Selected reaction monitoring for quantitative proteomics: A tutorial, Mol. Syst. Biol., 4, 1, 10.1038/msb.2008.61

Jorge, 2007, High-sensitivity analysis of specific peptides in complex samples by selected MS/MS ion monitoring and linear ion trap mass spectrometry: Application to biological studies, J. Mass Spectrom., 42, 1391, 10.1002/jms.1314

Carrera, 2011, Fast monitoring of species-specific peptide biomarkers using high-intensity-focused-ultrasound-assisted tryptic digestion and selected MS/MS ion monitoring, Anal. Chem., 83, 5688, 10.1021/ac200890w

Carrera, 2016, Protein biomarker discovery and fast monitoring for the identification and detection of Anisakids by parallel reaction monitoring (PRM) mass spectrometry, J. Proteom., 142, 130, 10.1016/j.jprot.2016.05.012

Gillet, 2012, Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: A new concept for consistent and accurate proteome analysis, Mol. Cell. Proteom., 11, O111.016717, 10.1074/mcp.O111.016717

Beynon, 2005, Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides, Nat. Methods, 2, 587, 10.1038/nmeth774

Bereman, 2012, The development of selected reaction monitoring methods for targeted proteomics via empirical refinement, Proteomics, 12, 1134, 10.1002/pmic.201200042

Aebersold, 2012, A computational tool to detect and avoid redundancy in selected reaction monitoring, Mol. Cell. Proteom., 11, 540, 10.1074/mcp.M111.013045

(2020, August 01). World Health Organization (WHO)/International Union of Immunological Societies (IUIS) Allergen Nomenclature Home Page. Available online: http://www.allergen.org.

Elsayed, 1975, The primary structure of allergen M from cod, Scand. J. Immunol., 4, 203, 10.1111/j.1365-3083.1975.tb02618.x

Aukrust, 1978, Crossed immunoelectrophoretic and crossed radioimmunoelectrophoretic studies employing a model allergen from codfish, Int. Arch. Allergy Appl. Immunol., 57, 253, 10.1159/000232110

Hordvik, 1996, Cloning of two distinct cDNAs encoding parvalbumin, the major allergen of Atlantic salmon (Salmo salar), Scand. J. Immunol., 44, 335, 10.1046/j.1365-3083.1996.d01-314.x

(2020, August 01). The Universal Protein Resource (Uniprot). Available online: http://www.uniprot.org/.

(2020, August 01). Allergome. The Platform for Allergen Knowledge. Available online: http://www.allergome.org/.

Aiello, 2015, A major allergen in rainbow trout (Oncorhynchus mykiss): Complete sequences of parvalbumin by MALDI tandem mass spectrometry, Mol. Biosyst., 11, 2373, 10.1039/C5MB00148J

Castellanos, 2015, Fish β-parvalbumin acquires allergenic properties by amyloid assembly, Swiss Med. Wkly., 145, w14128

Castro, 2016, The amyloid fold of Gad m 1 epitopes governs IgE binding, Sci. Rep., 6, 32801, 10.1038/srep32801

Carrera, 2019, Reconstruction of fish allergenicity from the content and structural traits of the component β-parvalbumin isoforms, Sci. Rep., 9, 16298, 10.1038/s41598-019-52801-6

Carrera, 2019, Molecular characterization of B-cell epitopes for the major fish allergen, parvalbumin, by shotgun proteomics, protein-based bioinformatics and IgE-reactive approaches, J. Proteom., 200, 123, 10.1016/j.jprot.2019.04.005

Carrera, 2012, Rapid direct detection of the major fish allergen, parvalbumin, by selected MS/MS ion monitoring mass spectrometry, J. Proteom., 75, 3211, 10.1016/j.jprot.2012.03.030

Sun, 2019, Development of a method for the quantification of fish major allergen parvalbumin in food matrix via liquid chromatography-tandem mass spectrometry with multiple reaction monitoring, Food Chem., 276, 358, 10.1016/j.foodchem.2018.10.014

Kuehn, 2013, Identification of enolases and aldolases as important fish allergens in cod, salmon and tuna: Component resolved diagnosis using parvalbumin and the new allergens, Clin. Exp. Allergy, 43, 811, 10.1111/cea.12117

Liu, 2012, Tilapia (Oreochromis mossambicus) allergens characterized by ELISA, SDS-PAGE, 2D gels, Western blotting and MALDI-TOF mass spectrometry, Int. J. Food Sci. Nutr., 63, 259, 10.3109/09637486.2011.619966

Rosmilah, 2013, Identification of parvalbumin and two new thermolabile major allergens of Thunnus tonggol using a proteomics approach, Int. Arch. Allergy Immunol., 162, 299, 10.1159/000354544

Liu, 2013, Tropomyosin from tilapia (Oreochromis mossambicus) as an allergen, Clin. Exp. Allergy, 43, 365, 10.1111/cea.12056

Veleiro, 2016, Are fish tropomyosins allergens?, Ann. Allergy Asthma Immunol., 116, 74, 10.1016/j.anai.2015.09.017

Carrera, 2018, Effects of high-pressure treatment on the muscle proteome of hake by bottom-up proteomics, J. Agric. Food Chem., 66, 4559, 10.1021/acs.jafc.8b00635

Hamada, 2001, Identification of collagen as a new fish allergen, Biosci. Biotechnol. Biochem., 65, 285, 10.1271/bbb.65.285

Cases, 2008, Identification of vitellogenin as an allergen in Beluga caviar allergy, Allergy, 6325, 479

Chai, 2005, Fish-borne parasitic zoonoses: Status and issues, Int. J. Parasitol., 35, 1233, 10.1016/j.ijpara.2005.07.013

EFSA (European Food Safety Authority) (2010). Scientific opinion on risk assessment of parasites in fishery products. EFSA J., 8, 1543.

Aibinu, 2019, Anisakis Nematodes in Fish and Shellfish—From infection to allergies, Int. J. Parasitol. Parasites Wildl., 9, 384, 10.1016/j.ijppaw.2019.04.007

Nieuwenhuizen, 2013, Anisakis: A food-borne parasite that triggers allergic host defences, Int. J. Parasitol., 43, 1047, 10.1016/j.ijpara.2013.08.001

Moen, 2016, Development of liquid chromatography-tandem mass spectrometry methods for the quantitation of Anisakis simplex proteins in fish, J. Chromatogr. A, 1432, 58, 10.1016/j.chroma.2016.01.002

Arcos, 2014, Proteomic profiling and characterization of differential allergens in the nematodes Anisakis simplex sensu stricto and A. pegreffii, Proteomics, 14, 1547, 10.1002/pmic.201300529

Polak, I., Łopieńska-Biernat, E., Stryiński, R., Mateos, J., and Carrera, M. (2020). Comparative Proteomics Analysis of Anisakis simplex s.s.-Evaluation of the Response of Invasive Larvae to Ivermectin. Genes, 11.

Lopata, 2016, Allergens and molecular diagnostics of shellfish allergy: Part 22 of the Series Molecular Allergology, Allergo J., 25, 210, 10.1007/s40629-016-0124-2

(2020, August 01). AllFam-The Database of Allergen Families. Available online: http://www.meduniwien.ac.at/allfam.

Laly, 2019, Identification of allergic proteins of Flower tail shrimp (Metapenaeus dobsonii), J. Food Sci. Technol., 56, 5415, 10.1007/s13197-019-04012-0

Yadzir, 2012, Identification of tropomyosin as major allergen of white squid (loligo edulis) by two-dimensional immunoblotting and mass spectrometry, Southeast Asian J. Trop. Med. Public Health, 43, 185

Lee, 2018, Identification of pyruvate kinase as a novel allergen in whiteleg shrimp (Litopenaeus vannamei) by specific-IgE present in patients with shrimp allergy, Food Chem., 258, 359, 10.1016/j.foodchem.2018.03.088

Wu, 2019, Identification of pyruvate kinase 2 as a possible crab allergen and analysis of allergenic proteins in crabs consumed in Taiwan, Food Chem., 289, 413, 10.1016/j.foodchem.2019.03.074

Ortea, 2009, Mass spectrometry characterization of species-specific peptides from arginine kinase for the identification of commercially relevant shrimp species, J. Proteome Res., 8, 5356, 10.1021/pr900663d

Khanaruksombat, 2014, Identification of a novel allergen from muscle and various organs in banana shrimp (Fenneropenaeus merguiensis), Ann. Allergy Asthma Immunol., 113, 301, 10.1016/j.anai.2014.06.002

Rosmilah, 2012, Identification of tropomyosin and arginine kinase as major allergens of Portunus pelagicus (blue swimming crab), Trop. Biomed., 29, 467

Fei, 2016, Assessment of the sensitizing capacity and allergenicity of enzymatic cross-linked arginine kinase, the crab allergen, Mol. Nutr. Food Res., 60, 1707, 10.1002/mnfr.201500936

Chen, 2013, Purification, physicochemical and immunological characterization of arginine kinase, an allergen of crayfish (Procambarus clarkii), Food Chem. Toxicol., 62, 475, 10.1016/j.fct.2013.09.014

Kamath, 2014, Effect of heat processing on antibody reactivity to allergen variants and fragments of black tiger prawn: A comprehensive allergenomic approach, Mol. Nutr. Food Res., 58, 1144, 10.1002/mnfr.201300584

Nugraha, 2018, Rapid and comprehensive discovery of unreported shellfish allergens using large-scale transcriptomic and proteomic resources, J. Allergy Clin. Immunol., 141, 1501, 10.1016/j.jaci.2017.11.028

Stella, 2020, LC-HRMS/MS for the simultaneous determination of four allergens in fish and swine food products, Food Chem., 331, 127276, 10.1016/j.foodchem.2020.127276

Meng, 2019, Detection of seven kinds of aquatic product allergens in meat products and seasoning by liquid chromatography-tandem mass spectrometry, J. Chromatogr., 37, 712

Korte, 2016, New High-Performance Liquid Chromatography Coupled Mass Spectrometry Method for the Detection of Lobster and Shrimp Allergens in Food Samples via Multiple Reaction Monitoring and Multiple Reaction Monitoring Cubed, J. Agric. Food Chem., 64, 6219, 10.1021/acs.jafc.6b02620

Rahman, 2010, Absolute quantification method and validation of airborne snow crab allergen tropomyosin using tandem mass spectrometry, Anal. Chim. Acta, 37, 712

Rahman, 2013, Comprehensive proteomics approach in characterizing and quantifying allergenic proteins from northern shrimp: Toward better occupational asthma prevention, J. Proteome Res., 12, 647, 10.1021/pr300755p

Ruethers, 2019, Variability of allergens in commercial fish extracts for skin prick testing, Allergy, 74, 1352, 10.1111/all.13748

Sorensen, 2017, Cross-reactivity in fish allergy: A double-blind placebo-controlled food challenge trial, J. Allergy Clin. Immunol., 140, 1170, 10.1016/j.jaci.2017.03.043

Asero, 2017, Shrimp Allergy: Analysis of commercially available extracts for in vivo diagnosis, Investig. Allergol. Clin. Immunol., 27, 175, 10.18176/jiaci.0127

Jappe, 2017, Relevance of lipophilic allergens in food allergy diagnosis, Curr. Allergy Asthma Rep., 17, 61, 10.1007/s11882-017-0731-0

Bonlokke, 2019, Exposures and Health Effects of Bioaerosols in Seafood Processing Workers—A Position Statement, J. Agromed., 24, 441, 10.1080/1059924X.2019.1646685