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Proteomics and Food Analysis: Principles, Techniques, and Applications
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Proteomics and Food Analysis: Principles, Techniques, and Applications

A special issue of Foods (ISSN 2304-8158). This special issue belongs to the section "Food Analytical Methods".

Deadline for manuscript submissions: closed (20 March 2021) | Viewed by 23223

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editor

Dr. Mónica Carrera

E-Mail Website
Guest Editor
Department of Food Technology, Spanish National Research Council (CSIC), Marine Research Institute (IIM), 36208 Vigo, Spain
Interests: proteomics; mass spectrometry; tandem mass spectrometry; proteins; food science and technology; molecular biology; food safety; confocal microscopy; food quality; food and nutrition
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The recent successes of proteomics methodologies make them a favorable strategy for food science studies, where research institutions, agencies, industries, and regulatory laboratories are combining efforts to acquire the needed knowledge on food composition, quality, safety, and bioactivity.

In this Special Issue, we will look at the latest advances in techniques and applications of proteomics in food analysis.

The latest advances in bottom–up proteomics techniques, shotgun proteomics, top–down proteomics, targeted proteomics, modoficomics, data-dependent acquisition (DDA), data-independent acquisition (DIA) strategies, and protein-chips/biosensors applied to food analysis are included in this Special Issue.

Thus, the power of these methodologies allows the food characterization, food authenticity, identification of quality markers, detection of food allergens, food microorganism detection, detection of food parasites, food processing analysis, identification and study of bioactive food compounds, bioinformatics analysis of food components and by-products, and the metabolic and systems biology study of food components from a nutritional or functional point of view, among others.

Dr. Mónica Carrera
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Foods is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Proteomics
  • Mass spectrometry
  • Systems biology
  • Food
  • Nutrition
  • Food quality
  • Food safety
  • Food bioactivity

Published Papers (7 papers)

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Editorial

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3 pages, 187 KiB  
Editorial
Proteomics and Food Analysis: Principles, Techniques, and Applications
by Mónica Carrera
Foods 2021, 10(11), 2538; https://doi.org/10.3390/foods10112538 - 22 Oct 2021
Cited by 4 | Viewed by 2312
Abstract
Proteomics can be considered the discipline of the large-scale analysis of proteins in a particular biological system [...] Full article
(This article belongs to the Special Issue Proteomics and Food Analysis: Principles, Techniques, and Applications)

Research

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15 pages, 1903 KiB  
Article
Sensopeptidomic Kinetic Approach Combined with Decision Trees and Random Forests to Study the Bitterness during Enzymatic Hydrolysis Kinetics of Micellar Caseins
by Dahlia Daher, Barbara Deracinois, Philippe Courcoux, Alain Baniel, Sylvie Chollet, Rénato Froidevaux and Christophe Flahaut
Foods 2021, 10(6), 1312; https://doi.org/10.3390/foods10061312 - 07 Jun 2021
Cited by 8 | Viewed by 2345
Abstract
Protein hydrolysates are, in general, mixtures of amino acids and small peptides able to supply the body with the constituent elements of proteins in a directly assimilable form. They are therefore characterised as products with high nutritional value. However, hydrolysed proteins display an [...] Read more.
Protein hydrolysates are, in general, mixtures of amino acids and small peptides able to supply the body with the constituent elements of proteins in a directly assimilable form. They are therefore characterised as products with high nutritional value. However, hydrolysed proteins display an unpleasant bitter taste and possible off-flavours which limit the field of their nutrition applications. The successful identification and characterisation of bitter protein hydrolysates and, more precisely, the peptides responsible for this unpleasant taste are essential for nutritional research. Due to the large number of peptides generated during hydrolysis, there is an urgent need to develop methods in order to rapidly characterise the bitterness of protein hydrolysates. In this article, two enzymatic hydrolysis kinetics of micellar milk caseins were performed for 9 h. For both kinetics, the optimal time to obtain a hydrolysate with appreciable organoleptic qualities is 5 h. Then, the influence of the presence or absence of peptides and their intensity over time compared to the different sensory characteristics of hydrolysates was studied using heat maps, random forests and regression trees. A total of 22 peptides formed during the enzymatic proteolysis of micellar caseins and influencing the bitterness the most were identified. These methods represent simple and efficient tools to identify the peptides susceptibly responsible for bitterness intensity and predict the main sensory feature of micellar casein enzymatic hydrolysates. Full article
(This article belongs to the Special Issue Proteomics and Food Analysis: Principles, Techniques, and Applications)
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21 pages, 5680 KiB  
Article
Proteomic Characterization of Bacteriophage Peptides from the Mastitis Producer Staphylococcus aureus by LC-ESI-MS/MS and the Bacteriophage Phylogenomic Analysis
by Ana G. Abril, Mónica Carrera, Karola Böhme, Jorge Barros-Velázquez, Benito Cañas, José-Luis R. Rama, Tomás G. Villa and Pilar Calo-Mata
Foods 2021, 10(4), 799; https://doi.org/10.3390/foods10040799 - 08 Apr 2021
Cited by 10 | Viewed by 2492
Abstract
The present work describes LC-ESI-MS/MS MS (liquid chromatography-electrospray ionization-tandem mass spectrometry) analyses of tryptic digestion peptides from phages that infect mastitis-causing Staphylococcus aureus isolated from dairy products. A total of 1933 nonredundant peptides belonging to 1282 proteins were identified and analyzed. Among them, [...] Read more.
The present work describes LC-ESI-MS/MS MS (liquid chromatography-electrospray ionization-tandem mass spectrometry) analyses of tryptic digestion peptides from phages that infect mastitis-causing Staphylococcus aureus isolated from dairy products. A total of 1933 nonredundant peptides belonging to 1282 proteins were identified and analyzed. Among them, 79 staphylococcal peptides from phages were confirmed. These peptides belong to proteins such as phage repressors, structural phage proteins, uncharacterized phage proteins and complement inhibitors. Moreover, eighteen of the phage origin peptides found were specific to S. aureus strains. These diagnostic peptides could be useful for the identification and characterization of S. aureus strains that cause mastitis. Furthermore, a study of bacteriophage phylogeny and the relationship among the identified phage peptides and the bacteria they infect was also performed. The results show the specific peptides that are present in closely related phages and the existing links between bacteriophage phylogeny and the respective Staphylococcus spp. infected. Full article
(This article belongs to the Special Issue Proteomics and Food Analysis: Principles, Techniques, and Applications)
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13 pages, 1812 KiB  
Article
Validation of a MS Based Proteomics Method for Milk and Egg Quantification in Cookies at the Lowest VITAL Levels: An Alternative to the Use of Precautionary Labeling
by Linda Monaci, Elisabetta De Angelis, Rocco Guagnano, Aristide P. Ganci, Ignazio Garaguso, Alessandro Fiocchi and Rosa Pilolli
Foods 2020, 9(10), 1489; https://doi.org/10.3390/foods9101489 - 19 Oct 2020
Cited by 21 | Viewed by 3261
Abstract
The prevalence of food allergy has increased over the last decades and consequently the food labeling policies have improved over the time in different countries to regulate allergen presence in foods. In particular, Reg 1169 in EU mandates the labelling of 14 allergens [...] Read more.
The prevalence of food allergy has increased over the last decades and consequently the food labeling policies have improved over the time in different countries to regulate allergen presence in foods. In particular, Reg 1169 in EU mandates the labelling of 14 allergens whenever intentionally added to foods, but the inadvertent contamination by allergens still remains an uncovered topic. In order to warn consumers on the risk of cross-contamination occurring in certain categories of foods, a precautionary allergen labelling system has been put in place by food industries on a voluntary basis. In order to reduce the overuse of precautionary allergen labelling (PAL), reference doses and action limits have been proposed by the Voluntary Incidental Trace Allergen Labelling VITAL project representing a guide in this jeopardizing scenario. Development of sensitive and reliable mass spectrometry methods are therefore of paramount importance in this regard to check the contamination levels in foods. In this paper we describe the development of a time-managed multiple reaction monitoring (MRM) method based on a triple quadrupole platform for milk and egg quantification in processed food. The method was in house validated and allowed to achieve levels of proteins lower than 0.2 mg of total milk and egg proteins, respectively, in cookies, challenging the doses recommended by VITAL. The method was finally applied to cookies labeled as milk and egg-free. This method could represent, in perspective, a promising tool to be implemented along the food chain to detect even tiny amounts of allergens contaminating food commodities. Full article
(This article belongs to the Special Issue Proteomics and Food Analysis: Principles, Techniques, and Applications)
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11 pages, 1401 KiB  
Article
Increasing Coverage of Proteome Identification of the Fruiting Body of Agaricus bisporus by Shotgun Proteomics
by Tae-Ho Ham, Yoonjung Lee, Soon-Wook Kwon, Myoung-Jun Jang, Youn-Jin Park and Joohyun Lee
Foods 2020, 9(5), 632; https://doi.org/10.3390/foods9050632 - 14 May 2020
Cited by 4 | Viewed by 2120
Abstract
To increase coverage of protein identification of an Agaricus bisporus fruiting body, we analyzed the crude protein fraction of the fruiting body by using a shotgun proteomics approach where 7 MudPIT (Multi-Protein identification Technology) runs were conducted and the MS/MS spectra from the [...] Read more.
To increase coverage of protein identification of an Agaricus bisporus fruiting body, we analyzed the crude protein fraction of the fruiting body by using a shotgun proteomics approach where 7 MudPIT (Multi-Protein identification Technology) runs were conducted and the MS/MS spectra from the 7 MudPIT runs were merged. Overall, 3093 non-redundant proteins were identified to support the expression of those genes annotated in the genome database of Agaricus bisporus. The physicochemical properties of the identified proteins, i.e., wide pI value range and molecular mass range, were indicative of unbiased protein identification. The relative quantification of the identified proteins revealed that K5XI50 (Aldedh domain-containing protein) and K5XEW1 (Ubiquitin-like domain-containing protein) were highly abundant in the fruiting body. Based on the information in the Uniprot (Universal Protein Resource) database for A. bisporus, only approximately 53% of the 3093 identified proteins have been functionally described and approximately 47% of the proteins remain uncharacterized. Gene Ontology analysis revealed that the majority of proteins were annotated with a biological process, and proteins associated with coiled-coil (12.8%) and nucleotide binding (8.21%) categories were dominant. The Kyoto Encyclopedia of Genes and Genome analysis revealed that proteins involved in biosynthesis of secondary metabolites and tyrosine metabolism were enriched in a fruiting body of Agaricus bisporus, suggesting that the proteins are associated with antioxidant metabolites. Full article
(This article belongs to the Special Issue Proteomics and Food Analysis: Principles, Techniques, and Applications)
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Review

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34 pages, 1078 KiB  
Review
Proteomic Insights into the Biology of the Most Important Foodborne Parasites in Europe
by Robert Stryiński, Elżbieta Łopieńska-Biernat and Mónica Carrera
Foods 2020, 9(10), 1403; https://doi.org/10.3390/foods9101403 - 03 Oct 2020
Cited by 16 | Viewed by 3775
Abstract
Foodborne parasitoses compared with bacterial and viral-caused diseases seem to be neglected, and their unrecognition is a serious issue. Parasitic diseases transmitted by food are currently becoming more common. Constantly changing eating habits, new culinary trends, and easier access to food make foodborne [...] Read more.
Foodborne parasitoses compared with bacterial and viral-caused diseases seem to be neglected, and their unrecognition is a serious issue. Parasitic diseases transmitted by food are currently becoming more common. Constantly changing eating habits, new culinary trends, and easier access to food make foodborne parasites’ transmission effortless, and the increase in the diagnosis of foodborne parasitic diseases in noted worldwide. This work presents the applications of numerous proteomic methods into the studies on foodborne parasites and their possible use in targeted diagnostics. Potential directions for the future are also provided. Full article
(This article belongs to the Special Issue Proteomics and Food Analysis: Principles, Techniques, and Applications)
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17 pages, 1139 KiB  
Review
Proteomic Strategies to Evaluate the Impact of Farming Conditions on Food Quality and Safety in Aquaculture Products
by Mónica Carrera, Carmen Piñeiro and Iciar Martinez
Foods 2020, 9(8), 1050; https://doi.org/10.3390/foods9081050 - 04 Aug 2020
Cited by 22 | Viewed by 5574
Abstract
This review presents the primary applications of various proteomic strategies to evaluate the impact of farming conditions on food quality and safety in aquaculture products. Aquaculture is a quickly growing sector that represents 47% of total fish production. Food quality, dietary management, fish [...] Read more.
This review presents the primary applications of various proteomic strategies to evaluate the impact of farming conditions on food quality and safety in aquaculture products. Aquaculture is a quickly growing sector that represents 47% of total fish production. Food quality, dietary management, fish welfare, the stress response, food safety, and antibiotic resistance, which are covered by this review, are among the primary topics in which proteomic techniques and strategies are being successfully applied. The review concludes by outlining future directions and potential perspectives. Full article
(This article belongs to the Special Issue Proteomics and Food Analysis: Principles, Techniques, and Applications)
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