Research

19 pages, 1858 KiB

Open AccessArticle

Identification of Potential Bioactive Peptides in Sheep Milk Kefir through Peptidomic Analysis at Different Fermentation Times

by Sevim Dalabasmaz, Esther Prados de la Torre, Sabrina Gensberger-Reigl, Monika Pischetsrieder and Manuel J. Rodríguez-Ortega

Foods 2023, 12(15), 2974; https://0-doi-org.brum.beds.ac.uk/10.3390/foods12152974 - 07 Aug 2023

Cited by 3 | Viewed by 1362

Abstract

Sheep farming is an important socioeconomic activity in most Mediterranean countries, particularly Spain, where it contributes added value to rural areas. Sheep milk is used in Spain mainly for making cheese, but it can be used also for making other dairy products, such [...] Read more.

Sheep farming is an important socioeconomic activity in most Mediterranean countries, particularly Spain, where it contributes added value to rural areas. Sheep milk is used in Spain mainly for making cheese, but it can be used also for making other dairy products, such as the lactic-alcoholic fermentation product known as kefir. Dairy products have health benefits because, among other reasons, they contain molecules with biological activity. In this work, we performed a proteomics strategy to identify the peptidome, i.e., the set of peptides contained in sheep milk kefir fermented for four different periods of time, aiming to understand changes in the pattern of digestion of milk proteins, as well as to identify potential bioactive peptides. In total, we identified 1942 peptides coming from 11 different proteins, and found that the unique peptides differed qualitatively among samples and their numbers increased along the fermentation time. These changes were supported by the increase in ethanol, lactic acid, and D-galactose concentrations, as well as proteolytic activity, as the fermentation progressed. By searching in databases, we found that 78 of the identified peptides, all belonging to caseins, had potential biological activity. Of these, 62 were not previously found in any milk kefir from other animal species. This is the first peptidomic study of sheep milk kefir comprising time-course comparison. Full article

(This article belongs to the Special Issue Application of Proteomics/Peptidomics in Foods)

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15 pages, 1730 KiB

Open AccessArticle

Impact of Bioinformatics Search Parameters for Peptides’ Identification and Their Post-Translational Modifications: A Case Study of Proteolysed Gelatines from Beef, Pork, and Fish

by Mouna Ambli, Barbara Deracinois, Anne-Sophie Jenequin, Rozenn Ravallec, Benoit Cudennec and Christophe Flahaut

Foods 2023, 12(13), 2524; https://0-doi-org.brum.beds.ac.uk/10.3390/foods12132524 - 28 Jun 2023

Viewed by 1260

Abstract

Bioinformatics software, allowing the identification of peptides by the comparison of peptide fragmentation spectra obtained by mass spectrometry versus targeted databases or directly by de novo sequencing, is now mandatory in peptidomics/proteomics approaches. Programming the identification software requires specifying, among other things, the [...] Read more.

Bioinformatics software, allowing the identification of peptides by the comparison of peptide fragmentation spectra obtained by mass spectrometry versus targeted databases or directly by de novo sequencing, is now mandatory in peptidomics/proteomics approaches. Programming the identification software requires specifying, among other things, the mass measurement accuracy of the instrument and the digestion enzyme used with the number of missed cleavages allowed. Moreover, these software algorithms are able to identify a large number of post-translational modifications (PTMs). However, peptide and PTM identifications are challenging in the agrofood field due to non-specific cleavage sites of physiological- or food-grade enzymes and the number and location of PTMs. In this study, we show the importance of customized software programming to obtain a better peptide and PTM identification rate in the agrofood field. A gelatine product and one industrial gelatine hydrolysate from three different sources (beef, pork, and fish), each digested by simulated gastrointestinal digestion, MS-grade trypsin, or both, were used to perform the comparisons. Two main points are illustrated: (i) the impact of the set-up of specific enzyme versus no specific enzyme use and (ii) the impact of a maximum of six PTMs allowed per peptide versus the standard of three. Prior knowledge of the composition of the raw proteins is an important asset for better identification of peptide sequences. Full article

(This article belongs to the Special Issue Application of Proteomics/Peptidomics in Foods)

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17 pages, 2766 KiB

Open AccessArticle

A Machine Learning Method to Identify Umami Peptide Sequences by Using Multiplicative LSTM Embedded Features

by Jici Jiang, Jiayu Li, Junxian Li, Hongdi Pei, Mingxin Li, Quan Zou and Zhibin Lv

Foods 2023, 12(7), 1498; https://0-doi-org.brum.beds.ac.uk/10.3390/foods12071498 - 02 Apr 2023

Cited by 2 | Viewed by 2216

Abstract

Umami peptides enhance the umami taste of food and have good food processing properties, nutritional value, and numerous potential applications. Wet testing for the identification of umami peptides is a time-consuming and expensive process. Here, we report the iUmami-DRLF that uses a logistic [...] Read more.

Umami peptides enhance the umami taste of food and have good food processing properties, nutritional value, and numerous potential applications. Wet testing for the identification of umami peptides is a time-consuming and expensive process. Here, we report the iUmami-DRLF that uses a logistic regression (LR) method solely based on the deep learning pre-trained neural network feature extraction method, unified representation (UniRep based on multiplicative LSTM), for feature extraction from the peptide sequences. The findings demonstrate that deep learning representation learning significantly enhanced the capability of models in identifying umami peptides and predictive precision solely based on peptide sequence information. The newly validated taste sequences were also used to test the iUmami-DRLF and other predictors, and the result indicates that the iUmami-DRLF has better robustness and accuracy and remains valid at higher probability thresholds. The iUmami-DRLF method can aid further studies on enhancing the umami flavor of food for satisfying the need for an umami-flavored diet. Full article

(This article belongs to the Special Issue Application of Proteomics/Peptidomics in Foods)

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19 pages, 6429 KiB

Open AccessArticle

Phosphoproteome Analysis Using Two-Dimensional Electrophoresis Coupled with Chemical Dephosphorylation

by Raquel Rodríguez-Vázquez, Daniel Mouzo and Carlos Zapata

Foods 2022, 11(19), 3119; https://0-doi-org.brum.beds.ac.uk/10.3390/foods11193119 - 07 Oct 2022

Cited by 3 | Viewed by 2459

Abstract

Protein phosphorylation is a reversible post-translational modification (PTM) with major regulatory roles in many cellular processes. However, the analysis of phosphoproteins remains the most challenging barrier in the prevailing proteome research. Recent technological advances in two-dimensional electrophoresis (2-DE) coupled to mass spectrometry (MS) [...] Read more.

Protein phosphorylation is a reversible post-translational modification (PTM) with major regulatory roles in many cellular processes. However, the analysis of phosphoproteins remains the most challenging barrier in the prevailing proteome research. Recent technological advances in two-dimensional electrophoresis (2-DE) coupled to mass spectrometry (MS) have enabled the identification, characterization, and quantification of protein phosphorylation on a global scale. Most research on phosphoproteins with 2-DE has been conducted using phosphostains. Nevertheless, low-abundant and low-phosphorylated phosphoproteins are not necessarily detected using phosphostains and/or MS. In this study, we report a comparative analysis of 2-DE phosphoproteome profiles using Pro-Q Diamond phosphoprotein stain (Pro-Q DPS) and chemical dephosphorylation of proteins with HF-P from longissimus thoracis (LT) muscle samples of the Rubia Gallega cattle breed. We found statistically significant differences in the number of identified phosphoproteins between methods. More specifically, we found a three-fold increase in phosphoprotein detection with the HF-P method. Unlike Pro-Q DPS, phosphoprotein spots with low volume and phosphorylation rate were identified by HF-P technique. This is the first approach to assess meat phosphoproteome maps using HF-P at a global scale. The results open a new window for 2-DE gel-based phosphoproteome analysis. Full article

(This article belongs to the Special Issue Application of Proteomics/Peptidomics in Foods)

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21 pages, 3703 KiB

Open AccessArticle

INFOGEST Digestion Assay of Raw and Roasted Hazelnuts and Its Impact on Allergens and Their IgE Binding Activity

by Ivana Prodić, Katarina Smiljanić, Christoph Nagl, Barbara Ballmer-Weber, Karin Hoffmann-Sommergruber and Tanja Ćirković Veličković

Foods 2022, 11(18), 2914; https://0-doi-org.brum.beds.ac.uk/10.3390/foods11182914 - 19 Sep 2022

Cited by 1 | Viewed by 1720

Abstract

Most of the food allergens sensitized via the gastrointestinal tract resist thermal treatments and digestion, particularly digestion by pepsin. Roasted hazelnuts are more commonly consumed than raw ones. Since no studies have characterized gastric digestion protein fragments of raw and roasted hazelnuts nor [...] Read more.

Most of the food allergens sensitized via the gastrointestinal tract resist thermal treatments and digestion, particularly digestion by pepsin. Roasted hazelnuts are more commonly consumed than raw ones. Since no studies have characterized gastric digestion protein fragments of raw and roasted hazelnuts nor their IgE binding properties, we compared these aspects of raw and roasted hazelnuts’ gastric digesta obtained by INFOGEST protocol. Their electrophoretically resolved profiles were probed with hazelnut allergic patients’ sera in 1D and 2D immunoblots. Electrophoretic profiles demonstrated pepsin digestion of all hazelnut allergens to varying extents. While 2D immunoblots indicated that roasting slightly reduced allergenicity, IgE ELISA with the pool of sera showed a slight significant (10%) increase in IgE binding in both gastric digesta. Cor a 9 isolated from the raw and roasted hazelnuts, characterized by far and near CD, remained stable after roasting, with preserved IgE reactivity. Its immunoreactivity contribution by inhibitory ELISA was noticeable in raw and roasted hazelnut digesta; its activity was slightly stronger in the roasted preparations. Roasting has a visible impact on proteins; however, it did not affect overall IgE reactivity. Gastric digestion slightly increases the overall IgE reactivity in raw and roasted hazelnuts, and may therefore impact the profiles of allergens and their fragments available to interact with the immune system in the small intestine. Full article

(This article belongs to the Special Issue Application of Proteomics/Peptidomics in Foods)

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18 pages, 3651 KiB

Open AccessArticle

The Investigation of Protein Profile and Meat Quality in Bovine Longissimus thoracic Frozen under Different Temperatures by Data-Independent Acquisition (DIA) Strategy

by Xia Li, Shuyi Qian, Feng Huang, Kaimin Li, Yu Song, Jiqian Liu, Yujie Guo, Chunhui Zhang and Christophe Blecker

Foods 2022, 11(12), 1791; https://0-doi-org.brum.beds.ac.uk/10.3390/foods11121791 - 17 Jun 2022

Cited by 4 | Viewed by 2338

Abstract

The influence of freezing on the protein profile and quality traits in bovine Longissimus thoracic (LT) muscle was investigated by the data-independent acquisition (DIA) technique. Compared to fresh meat, a total of 262 proteins were identified as differential abundance proteins (DAPs) in four [...] Read more.

The influence of freezing on the protein profile and quality traits in bovine Longissimus thoracic (LT) muscle was investigated by the data-independent acquisition (DIA) technique. Compared to fresh meat, a total of 262 proteins were identified as differential abundance proteins (DAPs) in four frozen groups (−12 °C, −18 °C, −38 °C, and −80 °C). According to the bioinformatics analysis, most of the DAPs in the significant Go terms and the KEGG pathway were structure proteins and enzymes. Proteome changes in the frozen bovine muscle at −12 °C and −18 °C were more significant than those at −38 °C and −80 °C. The result was consistent with the deterioration trend of the meat quality. The correlation analysis revealed that 17 proteins were correlated closely with the color, shear force, thawing loss, and cooking loss of the frozen meat, which could be used as putative biomarkers for frozen meat quality. MYO18A and ME3 are newly discovered proteins that are associated with frozen beef quality. In addition, CTTN and SERPINB6 were identified in frozen groups, which exhibited a significant inverse correlation with thawing loss (p < 0.01). These findings reveal the quality changes induced by freezing at the protein molecular level and provide new insights into the control of quality deterioration. Full article

(This article belongs to the Special Issue Application of Proteomics/Peptidomics in Foods)

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14 pages, 2599 KiB

Open AccessArticle

Fish Hydrolysate Supplementation Prevents Stress-Induced Dysregulation of Hippocampal Proteins Relative to Mitochondrial Metabolism and the Neuronal Network in Mice

by Julie Le Faouder, Bastien Arnaud, Régis Lavigne, Céline Lucas, Emmanuelle Com, Elodie Bouvret, Anne-Laure Dinel and Charles Pineau

Foods 2022, 11(11), 1591; https://0-doi-org.brum.beds.ac.uk/10.3390/foods11111591 - 28 May 2022

Cited by 2 | Viewed by 1966

Abstract

Over the past several decades, stress has dramatically increased in occidental societies. The use of natural resources, such as fish hydrolysates, may be an attractive strategy to improve stress management. Our previous study demonstrated the anxiolytic effects of fish hydrolysate supplementation in mice [...] Read more.

Over the past several decades, stress has dramatically increased in occidental societies. The use of natural resources, such as fish hydrolysates, may be an attractive strategy to improve stress management. Our previous study demonstrated the anxiolytic effects of fish hydrolysate supplementation in mice exposed to acute mild stress by limiting stress-induced corticosterone release and modulating the expression of a number of stress-responsive genes. Here, we explore hippocampal protein modulation induced by fish hydrolysate supplementation in mice submitted to acute mild stress, with the aim of better elucidating the underlying mechanisms. Hippocampi from the same cohort of Balb/c mice supplemented with fish hydrolysate (300 mg·kg⁻¹ body weight) or vehicle daily for seven days before being submitted or not to an acute mild stress protocol (four groups, n = 8/group) were subjected to label-free quantitative proteomics analysis combined with gene ontology data mining. Our results show that fish hydrolysate supplementation prevented the observed stress-induced dysregulation of proteins relative to mitochondrial pathways and the neuronal network. These findings suggest that fish hydrolysate represents an innovative strategy to prevent the adverse effects of stress and participate in stress management. Full article

(This article belongs to the Special Issue Application of Proteomics/Peptidomics in Foods)

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13 pages, 432 KiB

Open AccessArticle

Proteomic Profile of M. longissimus thoracis from Commercial Lambs Reared in Different Forage Systems

by Yangfan Ye, Evelyne Maes, Santanu Deb-Choudhury, Charles A. Hefer, Nicola M. Schreurs and Carolina E. Realini

Foods 2022, 11(10), 1419; https://0-doi-org.brum.beds.ac.uk/10.3390/foods11101419 - 13 May 2022

Cited by 1 | Viewed by 1552

Abstract

This study compared the protein composition of M. longissimus thoracis of lambs from six commercial forage production systems in New Zealand. A total of 286 proteins were identified based on liquid chromatography-tandem mass spectrometry. First, a binomial model showed that different production groups [...] Read more.

This study compared the protein composition of M. longissimus thoracis of lambs from six commercial forage production systems in New Zealand. A total of 286 proteins were identified based on liquid chromatography-tandem mass spectrometry. First, a binomial model showed that different production groups could be distinguished based on abundances of 16 proteins. Second, pair-wise comparisons were performed to search for protein abundance differences in meat due to animal sex (ewe vs. wether), diet (perennial ryegrass vs. chicory), and age (4 vs. 6–8 months old). Greater abundance of some myofibrillar and sarcoplasmic proteins were observed in lamb loins from ewes compared to wethers. Chicory diet and older age at slaughter were associated with meat with lower abundance of some myofibrillar proteins, possibly due to a greater proportion of muscle glycolytic fibres. The proteins that showed significant differences in their abundances due to production factors could be further investigated to understand their influence on meat quality. Full article

(This article belongs to the Special Issue Application of Proteomics/Peptidomics in Foods)

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14 pages, 2976 KiB

Open AccessArticle

Identification of Potential Peptide Marker(s) for Evaluating Pork Meat Freshness via Mass Spectrometry-Based Peptidomics during Storage under Different Temperatures

by Zhenqian Wei, Chen Dai, Anthony P. Bassey, Changbo Tang, Yu Han, Chong Wang and Guanghong Zhou

Foods 2022, 11(8), 1144; https://0-doi-org.brum.beds.ac.uk/10.3390/foods11081144 - 15 Apr 2022

Cited by 10 | Viewed by 2400

Abstract

This study applied peptidomics to investigate potential biomarkers for evaluating pork-meat freshness. The spoilage time points of pork meat stored at −2, 4, 10, and 25 °C were defined by evaluating meat freshness indicators (color, total viable count, pH, and total volatile basic [...] Read more.

This study applied peptidomics to investigate potential biomarkers for evaluating pork-meat freshness. The spoilage time points of pork meat stored at −2, 4, 10, and 25 °C were defined by evaluating meat freshness indicators (color, total viable count, pH, and total volatile basic nitrogen). Peptide MVHMASKE was identified as a potential peptide marker via multivariate analysis. Pearson correlation revealed a negative correlation between intensity of MVHMASKE and total viable count/total volatile basic nitrogen. In addition, the correlation between peptide content and the change in pork-meat freshness was verified using real-life samples, and the content of MVHMASKE showed a significant decline during storage under 4 and 25 °C, correspondingly reflecting the change of pork meat from fresh to spoiled. This study provides favorable evidence to evaluate pork-meat freshness by monitoring the change of peptide MVHMASKE in content based on mass spectrometry-based peptidomics. Full article

(This article belongs to the Special Issue Application of Proteomics/Peptidomics in Foods)

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