How germination time affects protein hydrolysis of lupins during gastroduodenal digestion and generation of resistant bioactive peptides

Germination time is a critical factor that influences the digestibility and bioactivity of proteins in pulses. The objective was to understand the effect of sprouting time on protein hydrolysis (PH) and the release of bioactive peptides during digestion of lupin (Lupinus angustifolius L.) to provide recommendations on the optimum germination time for maximum nutritional and health benefits. Protein hydrolysis was monitored during germination and digestion by gel electrophoresis, size exclusion chromatography, and the analysis of soluble protein (SP), peptides (PEP), free amino acids (FAA) and free amino groups. The anti-inflammatory activity of intestinal digests was investigated in cell culture assays. Peptidomic and in silico analyses of intestinal digesta were conducted to identify digestion-resistant bioactive fragments. Germination time increased SP, PEP, and FAA. During digestion, the PH and release of small peptides was higher in sprouted lupin than control flour. Intestinal digests from sprouted lupin flour for 7 days exhibited the highest anti-inflammatory activity. In this sample, 11 potential bioactive peptides were identified. These findings open the exploration of novel food formulations based on sprouted lupins with higher protein digestibility and health-promoting potential.

The physicochemical properties, functionality, and digestibility of hempseed protein isolate as impacted by spray drying and freeze drying

Hempseed protein has gained increasing attention for its sustainability and nourishment. This study aimed to investigate the effects of spray drying and freeze drying on the physicochemical properties, functionality, and digestibility of hempseed protein isolate (HPI). Compared to undried-HPI, both drying techniques altered physicochemical and structural properties. Particularly, protein denaturation temperature increased in freeze-dried HPI (FD-HPI) and spray-dried HPI (SD-HPI) samples (∼90 °C) than in undried-HPI (82.5 °C). Lysine content decreased from 38.26 mg/g in undried-HPI to 35.03 and 33.18 mg/g in FD-HPI and SD-HPI, respectively. Results revealed the loss of 26 and 17 kDa bands after drying. Notably, FD-HPI exhibited higher emulsifying stability and oil-holding capacity than SD-HPI. While both FD-HPI and SD-HPI had higher digestibility than undried-HPI, a 50% reduction in the liberation of free α-amino groups after digestion was found. This study provided information regarding changes in HPI after drying, offering insights for HPI production and application in the food industry.

Peptide-Based Mass Spectrometry for the Investigation of Protein Complexes

In the last two decades, biological mass spectrometry has become the gold standard for the identification of proteins in biological samples. The technological advancement of mass spectrometers and the development of methods for ionization, gas phase transfer, peptide fragmentation as well as for acquisition of high-resolution mass spectrometric data marked the success of the technique. This chapter introduces peptide-based mass spectrometry as a tool for the investigation of protein complexes. It provides an overview of the main steps for sample preparation starting from protein fractionation, reduction, alkylation and focus on the final step of protein digestion. The basic concepts of biological mass spectrometry as well as details about instrumental analysis and data acquisition are described. Finally, the most common methods for data analysis and sequence determination are summarized with an emphasis on its application to protein-protein complexes.

Proximate composition, microstructure, and protein and starch digestibility of seven collections of Jack bean (Canavalia ensiformis) with different optimal cooking times

Because of its high protein content, Jack bean (Canavalia ensiformis) is a promising alternative protein source. However, the utilization of Jack bean is limited due to the long cooking time to achieve palatable softness. We hypothesize that the cooking time may influence protein and starch digestibility. In this study, we characterized seven Jack bean collections with different optimal cooking times in terms of their proximate composition, microstructure and protein and starch digestibility. Kidney bean was included as a reference for microstructure and protein and starch digestibility. Proximate composition showed that Jack bean collections have a protein content ranging from 28.8 to 39.3%, a starch content ranging from 31 to 41%, a fiber content from 15.4 to 24.6%, and a concanavalin A content in the range 35-51 mg/g dry cotyledon. Particle sizes ranging between 125 and 250 µm were chosen as a representative sample of the whole bean to characterize microstructure and digestibility of the seven collections. Confocal laser microscopy (CLSM) revealed that Jack bean cells have an oval shape and contain starch granules embedded in a protein matrix similar to kidney bean cells. The diameter of Jack bean cells was measured by image analysis of CLSM micrographs and ranged from 103 to 123 µm, while the diameter of starch granules was 31-38 µm, comparatively larger than that of the kidney bean starch granules. Isolated intact cells were used to determine the starch and protein digestibility in the Jack beans collections. The digestion kinetics of starch followed a logistic model, whereas the digestion kinetics of protein followed a fractional conversion model. We found no correlation between optimal cooking time and kinetic parameters of protein and starch digestibility, implying that optimal cooking time is not predictive of protein and starch digestibility. In addition, we tested the effect of reduced cooking times on protein and starch digestibility on one Jack bean collection. The result showed that reducing cooking time significantly reduces starch digestibility, but not protein digestibility. The present study contributes to our understanding of the effect of food processing on protein and starch digestibility in legumes.

Plant-based meat analogs and fat substitutes, structuring technology and protein digestion: A review

There is currently an increasing trend in the consumption of meat analogs and fat substitutes due to the health hazards by excessive consumption of meat. Simulating the texture and mouthfeel of meat through structured plant-derived polymers has become a popular processing method. In this review, the mechanical structuring technology of plant polymers for completely replacing real meat is mainly introduced in this review, which mainly focuses on the parameters and principles of mechanical equipment for the production of vegan meat. The difference in composition between plant meat and real meat is mainly reflected in the protein, and particular attention should be paid to the digestive characteristics of plant meat protein in the gastrointestinal tract. Therefore, the differences in the protein digestibility properties of meat analogs and real meat is discussed in this review, focusing primarily on protein digestibility and peptide/amino acid composition of mechanically structured vegan meats. In terms of fat substitutes for meat products, the types of plant polymer colloidal systems used for meat fat substitutes is comprehensively introduced, including emulsion, hydrogel and oleogel.

A multi-centre peptidomics investigation of food digesta: current state of the art in mass spectrometry analysis and data visualisation

Mass spectrometry has become the technique of choice for the assessment of a high variety of molecules in complex food matrices. It is best suited for monitoring the evolution of digestive processes in vivo and in vitro. However, considering the variety of equipment available in different laboratories and the diversity of sample preparation methods, instrumental settings for data acquisition, statistical evaluations, and interpretations of results, it is difficult to predict a priori the ideal parameters for optimal results. The present work addressed this uncertainty by executing an inter-laboratory study with samples collected during in vitro digestion and presenting an overview of the state-of-the-art mass spectrometry applications and analytical capabilities available for studying food digestion. Three representative high-protein foods - skim milk powder (SMP), cooked chicken breast and tofu - were digested according to the static INFOGEST protocol with sample collection at five different time points during gastric and intestinal digestion. Ten laboratories analysed all digesta with their in-house equipment and applying theirconventional workflow. The compiled results demonstrate in general, that soy proteins had a slower gastric digestion and the presence of longer peptide sequences in the intestinal phase compared to SMP or chicken proteins, suggesting a higher resistance to the digestion of soy proteins. Differences in results among the various laboratories were attributed more to the peptide selection criteria than to the individual analytical platforms. Overall, the combination of mass spectrometry techniques with suitable methodological and statistical approaches is adequate for contributing to the characterisation of the recently defined digestome.

Digestion of human milk processed by high pressure processing and Holder pasteurization using a dynamic in vitro model of the preterm infant

Holder pasteurization (HoP) (62.5 °C, 30 min) of donor human milk is widely used to inactivate potential pathogens but may lead to denaturation and aggregation of bioactive proteins, reducing their functionality. In contrast, high pressure processing (HPP) is a non-thermal technique that minimally affects assessed bioactive components; however, it is unclear how HPP affects protein digestion, and retention of functional bioactive proteins. Raw or processed (HoP; HPP[500 MPa,10 min]) pools of milk (N = 3, from 9 donors) were subjected in triplicate to in vitro digestion simulating the preterm infant gastrointestinal tract. Compared to raw or HPP, HoP increased intestinal proteolysis of lactoferrin and bioactive milk fat globule membrane proteins. Lysozyme activity was impacted by digestion following HoP (72 % to 7 %)-significantly more than HPP (75 % to 34 %) or raw (100 % to 39 %), which did not differ. Proteins in HPP-treated donor milk are digested no different than raw milk, while preserved bioactivity remains functional upon digestion.

An innovative insecticidal approach based on plant protease inhibitor and Bt protoxins inhibits trypsin-like activity in zebrafish

The Leucaena leucocephala trypsin inhibitor (LTI) + Bacillus thuringiensis (Bt) protoxins mix has been proposed as a novel larvicide agent in order to control the vector mosquito of dengue virus, Aedes aegypti, in their aquatic breeding sites. However, use of this insecticide formulation has raised concerns about its impacts on aquatic biota. In this context, this work aimed to assess the effects of LTI and Bt protoxins, separately or in combination, in zebrafish, in regard to the evaluation of toxicity at early life stages and to the presence of LTI inhibitory effects on intestinal proteases of this fish. Results showed that LTI and Bt concentrations (250 mg/L, and 0.13 mg/L, respectively), and LTI + Bt mix (250 mg/L + 0.13 mg/L) - 10 times superior to those with insecticidal action - did not cause death nor did it induce morphological changes during embryonic and larval development (3 to 144 h post-fertilization) of zebrafish. Molecular docking analyses highlighted a possible interaction between LTI and zebrafish trypsin, especially through hydrophobic interactions. In concentrations near to those with larvicidal action, LTI (0.1 mg/mL) was able to inhibit in vitro intestinal extracts of trypsin in female and male fish by 83 % and 85 %, respectively, while LTI + Bt mix promoted trypsin inhibition of 69 % in female and 65 % in male ones. These data show that the larvicidal mix can potentially promote deleterious effects to nutrition and survival in non-target aquatic organisms, especially those with trypsin-like dependent protein digestion.

Membrane filtration processing of infant milk formula alters protein digestion in young pigs

Reducing heat treatment (HT) during processing of infant milk formula (IMF) is desirable to produce a product that more closely resembles breast milk. By employing membrane filtration (MEM), we produced an IMF (60:40 whey to casein ratio) at pilot scale (250 kg). MEM-IMF had a significantly higher content of native whey (59.9 %) compared to HT-IMF (4.5 %) (p < 0.001). Pigs, at 28 days old, were blocked by sex, weight and litter origin and assigned to one of two treatments (n = 14/treatment): (1) starter diet containing 35 % of HT-IMF powder or (2) starter diet containing 35 % of MEM-IMF powder for 28 days. Body weight and feed intake were recorded weekly. Pigs at day 28 post weaning were sacrificed 180 min after their final feeding, for the collection of gastric, duodenal, jejunum and ileal contents (n = 10/treatment). MEM-IMF diet resulted in more water-soluble proteins and higher levels of protein hydrolysis in the digesta at various gut locations compared to HT-IMF (p < 0.05). In the jejunal digesta, a higher concentration of free amino acids were present post MEM-IMF consumption (247 ± 15 µmol g^-1 of protein in digesta) compared to HT-IMF (205 ± 21 µmol g^-1 of protein). Overall, average daily weight gain, average dairy feed intake and feed conversion efficiency were similar for pigs fed either MEM-IMF or HT-IMF diets, but differences and trends to difference of these indicators were determined in particular intervention periods. In conclusion, reducing heat treatment during processing of IMF influenced protein digestion and revealed minor effects on growth parameters providing in vivo evidence that babies who are fed with IMF processed by MEM are likely to have different protein digestion kinetics but minimal effect on overall growth trajectories as babies fed IMF processed by traditional thermal processing.

Bioprospecting for fungal enzymes for applications in microalgal biomass biorefineries

Microalgal biomass is a promising feedstock for biofuels, feed/food, and biomaterials. However, while production and commercialization of single-product commodities are still not economically viable, obtaining multiple products in a biomass biorefinery faces several techno-economic challenges. The aim of this study was to identify a suitable source of hydrolytic enzymes for algal biomass saccharification. Screening of twenty-six fungal isolates for secreted enzymes activity on Chlamydomonas reinhardtii biomass resulted in the identification of Aspergillus niger IB-34 as a candidate strain. Solid-state fermentation on wheat bran produced the most active enzyme preparations. From sixty-five proteins identified by liquid chromatography coupled to mass spectrometry (LC-MS) (ProteomeXchange, identifier PXD034998) from A. niger IB-34, the majority corresponded to predicted secreted proteins belonging to the Gene Ontology categories of catalytic activity/hydrolase activity on glycosyl and O-glycosyl compounds. Skimmed biomass of biotechnologically relevant strains towards the production of commodities, Chlorella sorokiniana and Scenedesmus obliquus, was fully saccharified after a mild pretreatment at 80 °C for 10 min, at a high biomass load of 10% (w/v). The soluble liquid stream, after skimming and saccharification of biomass of both strains, was further converted into ethanol by fermentation with Saccharomyces cerevisiae at a theoretical maximum efficiency, in a separated saccharification and fermentation assays. The resulting insoluble protein, after biomass skimming with an organic solvent and enzymatic saccharification, was highly digestible in an in vitro digestion assay. Proof of concept is presented for an enzyme-assisted biomass biorefinery recovering 81% of the main biomass fractions in a likely suitable form for the conversion of lipids and carbohydrates into biofuels and proteins into feed/food. KEY POINTS: • Twenty-six fungal extracts were analyzed for saccharification of microalgal biomass. • Skimmed biomass was fully enzymatically saccharified and fermented into ethanol. • Up to 81% recovery of biomass fractions suitable for biofuels and feed/food.

Thiol-ene-based microfluidic chips for glycopeptide enrichment and online digestion of inflammation-related proteins osteopontin and immunoglobulin G

Proteins, and more specifically glycoproteins, have been widely used as biomarkers, e.g., to monitor disease states. Bottom-up approaches based on mass spectrometry (MS) are techniques commonly utilized in glycoproteomics, involving protein digestion and glycopeptide enrichment. Here, a dual function polymeric thiol-ene-based microfluidic chip (TE microchip) was applied for the analysis of the proteins osteopontin (OPN) and immunoglobulin G (IgG), which have important roles in autoimmune diseases, in inflammatory diseases, and in coronavirus disease 2019 (COVID-19). TE microchips with larger internal surface features immobilized with trypsin were successfully utilized for OPN digestion, providing rapid and efficient digestion with a residence time of a few seconds. Furthermore, TE microchips surface-modified with ascorbic acid linker (TEA microchip) have been successfully utilized for IgG glycopeptide enrichment. To illustrate the use of the chips for more complex samples, they were applied to enrich IgG glycopeptides from human serum samples with antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The dual functional TE microchips could provide high throughput for online protein digestion and glycopeptide enrichment, showing great promise for future extended applications in proteomics and the study of related diseases.

Protein Digestion for 2D-DIGE Analysis

In-gel digestion of protein spots derived from two-dimensional gels and their subsequent identification by mass spectrometry is involved in a multitude of mass spectrometry-driven proteomic experiments, including fluorescence two-dimensional difference gel electrophoresis (2D-DIGE). This type of proteomic methodology has been involved in the establishment of comparative proteome maps and in the identification of differentially expressed proteins and their isoforms in health and disease. Most in-gel digestion protocols follow a number of common steps including excision of the protein spots of interest, destaining, reduction and alkylation (for silver-stained gels), and dehydration and overnight digestion with the proteolytic enzyme of choice. While trypsin has been a mainstay of peptide digestion for many years, it does have its shortcomings, particularly related to incomplete peptide digestion, and this has led to a rise in popularity for other proteolytic enzymes either used alone or in combination. This chapter discusses the alternative enzymes available and describes the process of in-gel digestion using the enzyme trypsin.

Two-Dye Versus Three-Dye DIGE for Comparative Testis Tissue Proteomic Analysis

The global analysis of the proteome is an important tool in cell biology. Comparative proteomic evaluations can identify and compare the composition, dynamics, and modifications between different samples. Comparing tissue proteomes under different conditions is crucial for advancing the biomedical field. Fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) is a sensitive and robust biochemical method that can compare multiple protein samples over a broad dynamic range on the same analytical gel and can be used to establish differentially expressed protein profiles between different sample groups. 2D-DIGE involves fluorescently labeling protein samples with CyDye flours, via a two-dye or a three-dye system, pre-separation by isoelectric point, and molecular weight. DIGE circumvents gel-to-gel variability by multiplexing samples to a single gel and through the use of a pooled internal standard for normalization, thus enabling accurate high-resolution analysis of differences in protein abundance between samples. This chapter discusses 2D-DIGE as a comparative tissue proteomic technique and describes in detail the experimental steps required for comparative proteomic analysis employing both options of two-dye and three-dye DIGE minimal labeling.

Clinical Proteomics: Liquid Chromatography-Mass Spectrometry (LC-MS) Purification Systems

Liquid chromatography/mass spectrometry (LC/MS) has become a routine powerful technology in clinical proteomic studies for protein identification, protein characterization, and the discovery of biomarkers. In this chapter, we describe two protocol methods to analyze clinical patient samples using a resin-based depletion column followed by either protein In-Gel enzymatic digestion or protein In-Solution enzymatic digestion using a simple kit-based approach (i.e., using the PreOmics iST sample preparation kit), followed by analysis using one-dimensional reverse-phase chromatography (RPC) or high pH reversed-phase peptide fractionation.

A proteomics approach reveals digestive and nutritional responses to food intake in anadromous Coilia nasus

The estuarine tapertail anchovy, Coilia nasus, is an anadromous fish that undertakes over a 600-km spawning migration along the Yangtze River of China. They generally cease feeding during this process, but we recently documented that a small proportion of them appear to feed. Research on proteomic responses is essential for understanding the phenomenon of C. nasus feeding. In this study, we used an iTRAQ-based proteomics approach to study the changes in protein expression in response to food intake in C. nasus following voluntary fasting. Coilia nasus in the feeding group (CSI) were fed shrimp or small fish, whereas those in the control group (CSN) were starved. We identified 3279 proteins in the gastric tissue/stomach, of which 279 were significantly differentially expressed. In all, 133 differentially expressed proteins (DEPs) were upregulated and 146 proteins were downregulated in CSI compared with those in CSN C. nasus. In addition to gastric acid secretion caused by gastric distention, a functional analysis suggested that a series of DEPs were involved mainly in the regulation of protein digestion (e.g., carboxypeptidase A1 and chymotrypsin A-like), immune response (e.g., lysozyme and alpha 2-macroglobulin), and nutrition metabolism (e.g., glyceraldehyde 3-phosphate dehydrogenase, glycogenin, long-chain acyl-CoA synthetase, and creatine kinase). Real-time PCR confirmed that the mRNA levels of the DEPs were similar those obtained using iTRAQ. These results indicate that the nutrients obtained through food were effectively utilized by C. nasus, thereby providing energy for swimming, gonadal maturation, primary metabolism, and an enhanced immune function to better resist pathogen interference. This research contributes to the elucidation of nutritional regulation mechanisms of C. nasus to better protect the wild population.

In vivo absorptomics: Identification of bovine milk-derived peptides in human plasma after milk intake

A dedicated two-step purification procedure prior to nanoliquid chromatography-electrospray-tandem mass spectrometry analysis enabled the identification of bovine milk-derived peptides absorbed and circulating in the plasma of three healthy volunteers who received 250 mL of pasteurized milk after a 10-days washout. The appearance and clearance of milk peptides in plasma were monitored at various time points. Overall, 758, 273 and 212 unique peptides derived from 15, 15 and 18 bovine milk proteins, respectively, were identified in the plasma of these volunteers, evidencing a substantial inter-individual variability. Peptides encrypting possible bioactive and/or immunogenic molecules originating from caseins, β-lactoglobulin and minor milk proteins were detected. Peptide representation data revealed the combined action of endoproteases involved in primary hydrolysis during gastroduodenal digestion and exopeptidases that hydrolyse peptides in the small intestine. It remains to be established whether the half-life and concentration ranges of circulating milk-derived peptides may have any impacts on human health.

Non-invasive monitoring of in vitro gastric milk protein digestion kinetics by 1H NMR magnetization transfer

Processing of milk involves heating, which can modify the structure and digestibility of its proteins. In vitro models are useful for studying protein digestion. However, validating these models with in vivo data is challenging. Here, we non-invasively monitor in vitro gastric milk protein digestion by protein-water chemical exchange detected by ¹H nuclear magnetic resonance (NMR) magnetization transfer (MT). We obtained either a fitted composite exchange rate (CER) with a relative standard error of ≤10% or the MT ratio (MTR) of the intensity without or with an off-resonance saturation pulse, from just a single spectral acquisition. Both CER and MTR, affected by the variation in the amount of semi-solid protons, decreased during in vitro gastric digestion in agreement with standard protein content analyses. The decrease was slower in heated milk, indicating slower breakdown of the coagulum. Our results open the way to future quantification of protein digestion in vivo by MRI.

Structural and chemical changes induced by temperature and pH hinder the digestibility of whey proteins

In the food and feed industry, protein extraction is commonly performed under acid or basic conditions, combined with heat, in order to increase the extraction yield. Under severe processing conditions, proteins may undergo molecular modifications. Here, the effects of heating (30, 60, 90 °C) at different pH values (2, 7, 9, 11, 13) were evaluated on commercial whey proteins, used as a simplified protein model. The main structure and chemical modifications concerning protein aggregation, hydrolysis, insolubilization, amino acid degradation and racemization were investigated in detail. Using in vitro static models, the degree of protein hydrolysis and the released peptides were determined after the digestive process. Accumulation of molecular modifications was mostly observed after basic pH and high temperatures treatments, together with a marked decrease and modification of the digestibility profile. Instead, protein digestibility increased in neutral and acidic conditions in a temperature-dependent manner, even if some modification in the structure occurs.

In vitro gastro-small intestinal digestion of conventional and mildly processed pea protein ingredients

We report on the effect of processing, particularly heating, on the digestion dynamics of pea proteins using the standardised semi-dynamic in vitro digestion method. Fractions with native proteins were obtained by mild aqueous fractionation of pea flour. A commercial pea protein isolate was chosen as a benchmark. Heating dispersions of pea flour and mild protein fractions reduced the trypsin inhibitory activity to levels similar to that of the protein isolate. Protein-rich and non-soluble protein fractions were up to 18% better hydrolysed after being thermally denatured, particularly for proteins emptied later in the gastric phase. The degree of hydrolysis throughout the digestion was similar for these heated fractions and the conventional isolate. Further heating of the protein isolate reduced its digestibility as much as 9%. Protein solubility enhances the digestibility of native proteins, while heating aggregates the proteins, which ultimately reduces the achieved extent of hydrolysis from gastro-small intestinal enzymes.

Chew on it: influence of oral processing behaviour on in vitro protein digestion of chicken and soya-based vegetarian chicken

Oral processing behaviour can affect the bioavailability of macronutrients. The aim of the present study was to determine the influence of oral processing behaviour on bolus properties and in vitro protein digestion of chicken and soya-based vegetarian chicken. Natural chewing time and chewing frequency of both foods were determined in healthy adults (n 96). While natural chewing time differed considerably between consumers (chicken: 7·7-39·4 s; soya-based vegetarian chicken: 7·8-46·2 s), chewing frequency (1·4 chews/s) did not differ considerably between consumers and was independent of product type. Natural chewing times of 11 and 24 s were found for clusters of consumers showing shortest and longest chewing time for both products. Chicken and soya-based vegetarian chicken were chewed for 11 and 24 s and boli expectorated by n 16 consumers to determine in vitro gastric digestion and by n 7 to determine in vitro intestinal digestion. For both foods, longer chewing time resulted in the formation of significantly (P < 0·05) more and smaller bolus fragments and higher in vitro degree of protein hydrolysis (DH%) than shorter chewing time (chicken: DH%11s = 7 ± 23 % and DH%24s = 89 ± 26 %; soya-based vegetarian chicken: DH%11s = 57 ± 18 % and DH%24s = 70 ± 21 %, P < 0·001). In vitro degree of protein hydrolysis was higher for chicken than that for soya-based vegetarian chicken regardless of chewing time. We conclude that naturally occurring longer chewing time leads to more and smaller bolus particles of chicken and soya-based vegetarian chicken and thereby increases in vitro protein hydrolysis compared with shorter chewing time.

Dual effects of quercetin on protein digestion and absorption in the digestive tract

Quercetin is a well-studied natural product with multiple pharmacological properties. In this study, we demonstrated that quercetin suppressed protein digestion in the intestinal fluid by inhibiting trypsin, a key digestive enzyme. However, we also observed a previously unknown property of quercetin: promoting the intestinal absorption of proteins. In addition, the promoted protein absorption was mediated by internalization of digested oligopeptides in the intestinal epithelia rather than increasing the intestinal paracellular permeability. Notably, four other flavonoids also achieved such enhanced intestinal absorption, suggesting that this effect was associated with the aglycone flavonol backbone, but not related to their inhibitory potencies against trypsin. This study demonstrates that quercetin exhibits dual effects on protein digestion and absorption: 1) suppressing protein digestion by inhibiting trypsin in the intestinal fluid; 2) promoting the intestinal absorption of oligopeptides in the intestinal villi cells.

Digestibility and gastrointestinal fate of meat versus plant-based meat analogs: An in vitro comparison

Plant-based meat analogs are likely to have different gastrointestinal fates than real meat products due to differences in their compositions and structures. Here, we compared the gastrointestinal fate of ground beef and ground beef analogs using the INFOGEST in vitro digestion model, focusing on differences in microstructure, physicochemical properties, lipid digestion, and protein digestion in different regions of the model gut. The presence of dietary fibers in the beef analogs increased their apparent shear viscosity in the gastrointestinal fluids, which may have inhibited lipid digestion in the small intestine. The proteins in the beef analogs were digested more rapidly in the stomach but less rapidly in the small intestine, which may have been due to differences in protein type (globular soy versus fibrous beef proteins), structural organization, and the presence of dietary fibers in the meat analogs.

Soybean germination limits the role of cell wall integrity in controlling protein physicochemical changes during cooking and improves protein digestibility

Previous studies showed that in vitro digestibility of proteins in cooked beans is modulated by heat treatment and that the effect may be different whether proteins are heated in intact cotyledon or in a bean flour. In this study, germinated and non-germinated soybean cotyledons and flour were boiled at 100 °C for varying times (30, 90, or 180 min). After grinding, the level of trypsin inhibitors, protein aggregation, surface hydrophobicity, the secondary structure, and in vitro digestibility were studied. The presence of an intact cell wall during cooking increased protein denaturation temperature by about 10% and reduced the denaturation of trypsin inhibitors, and induced distinct changes in protein surface hydrophobicity and secondary structure. These physicochemical properties translated into an increment in protein degree of hydrolysis (DH, 72%) of protein cooked for 30 min as flour compared to proteins cooked in intact soybean tissues (64%). Increase in cooking times (90 and 180 min) resulted in limited improvement in the protein digestibility and changes in protein physicochemical properties for both boiled cotyledons and flour. Soybean germination resulted in distinct changes in protein physicochemical properties and higher protein DH% of raw soybean (61%) compared to non-germinated raw soybean (36%). An increase in protein digestibility of germinated soybean was also observed after boiling for both cotyledon and flour. However, significant differences in DH% were not observed between proteins boiled in intact cotyledon and in a flour. This work provides extra knowledge of the role of cellular integrity on protein properties in plant foods and suggests that germination or grinding before cooking may increase protein digestibility.

Proteolysis of whey protein isolates in nanoemulsion systems: Impact of nanoemulsification and additional synthetic emulsifiers

Nanoemulsions are currently of interest in the functional food sector because their small droplet size (100-500 nm) provides a number of potential advantages over conventional emulsions. This study concerned the behavior of nanoemulsions stabilized with whey proteins and two synthetic emulsifiers (Tween 80 and Croduret), and exposed to conditions simulating the human upper gastrointestinal tract. In particular, the effect of synthetic emulsifiers (food additives) on the interfacial composition and digestion rate of milk proteins at the interface of nanoemulsions was determined. The results indicate that the protein was partially co-absorbed with only one synthetic emulsifier (Croduret) at the interface, which made protein more resistant to digestion in the nanoemulsion system. This suggests that the degree of protein digestion can be controlled by appropriate selection of synthetic emulsifiers and presenting the protein in nanoemulsion system.

Development of a sample preparation approach for the analysis of fining agents in wines by liquid chromatography with tandem mass spectrometry

During winemaking a wide variety of processing aids such as albumin, caseinates and lysozyme are often used. These proteins are considered allergenic and could become a human health risk in susceptible individuals. In our knowledge, there are no methods published for the analysis of these three proteins simultaneously by liquid chromatography with tandem mass spectrometry, with electrospray ionization. Therefore, in this work, a sample preparation approach for the analysis of α-casein, β-casein, albumin and lysozyme, in a single run, was performed and compared with published data. Through a pH adjustment, combining the use of cellulose ester membranes, a precipitation with organic solvents and a final concentration/clean-up, we achieved recovery values from 90.7 to 108.6%. The method was validated, showing determination coefficients R² ≥ 0.99. This method was able to quantify proteins even at lower levels (limits of quantification from 0.01 to 0.25 mg/L) than the current legal limits.

Nucleic acid sample preparation from whole blood in a paper microfluidic device using isotachophoresis

Nucleic acid amplification tests (NAATs) are a crucial diagnostic and monitoring tool for infectious diseases. A key procedural step for NAATs is sample preparation: separating and purifying target nucleic acids from crude biological samples prior to nucleic acid amplification and detection. Traditionally, sample preparation has been performed with liquid- or solid-phase extraction, both of which require multiple trained user steps and significant laboratory equipment. The challenges associated with sample preparation have limited the dissemination of NAAT point-of-care diagnostics in low resource environments, including low- and middle-income countries. We report on a paper-based device for purification of nucleic acids from whole blood using isotachophoresis (ITP) for point-of-care NAATs. We show successful extraction and purification of target nucleic acids from large volumes (33 µL) of whole human blood samples with no moving parts and few user steps. Our device utilizes paper-based buffer reservoirs to fully contain the liquid ITP buffers and does not require complex filling procedures, instead relying on the natural wicking of integrated paper membranes. We perform on-device blood fractionation via filtration to remove leukocytes and erythrocytes from our sample, followed by integrated on-paper proteolytic digestion of endogenous plasma proteins to allow for successful isotachophoretic extraction. Paper-based isotachophoresis purifies and concentrates target nucleic acids that are added directly to recombinase polymerase amplification (RPA) reactions. We show consistent amplification of input copy concentrations of as low as 3 × 10³ copies nucleic acid per mL input blood with extraction and purification taking only 30 min. By employing a paper architecture, we are able to incorporate these processes in a single, robust, low-cost design, enabling the direct processing of large volumes of blood, with the only intermediate user steps being the removal and addition of tape. Our device represents a step towards a simple, fully integrated sample preparation system for nucleic acid amplification tests at the point-of-care.

Self-assembly synthes is of trypsin-immobilized monolithic microreactor for fast and efficient proteolysis

Fast and highly efficient digestion of proteins is essential for high-throughput proteomic analysis. Herein, a facile approach was developed for self-assembly preparation of trypsin-immobilized capillary monolithic column and its application as an immobilized enzyme microreactor (IMER) for fast and highly efficient proteolysis was described. The performance of the trypsin-immobilized monolithic enzyme microreactor was evaluated by in-situ digestion of model proteins. The results showed that the trypsin-immobilized monolithic enzyme microreactor had much higher tryptic digestion efficiency than the free trypsin in solution, where the coverage of peptide sequences by mass spectrometry (MS)-based analysis could bear comparison with the free one, while the digestion time was dramatically shortened from 12 h to 16 s. Furthermore, the trypsin-immobilized monolithic enzyme microreactor also exhibited good practicability to complex human serum sample, in which the total of 45 peptides from human serum albumin (HSA) matched with sequence coverage of 75% were precisely identified. The successful application demonstrated the promising potential of the trypsin-immobilized capillary monolithic column as the IMER in high-throughput proteomic analysis.

In vitro starch and protein digestion kinetics of cooked Bambara groundnuts depend on processing intensity and hardness sorting

When pulse seeds from a single batch are cooked, considerable variability of hardness values in the population is usually observed. Sorting the seeds into hardness categories could reduce the observed diversity and increase uniformity. Therefore, we investigated the effect of processing intensity whether or not combined with sorting into hardness categories on the in vitro starch and protein digestion kinetics of cooked Bambara groundnuts (cooking times 40 min and 120 min). The average hardness values were 89 ± 32 N and 42 ± 20 N for 40 min and 120 min cooking time, respectively. The high standard deviation of hardness for each cooking time revealed a high level of diversity amongst the seeds. Individual cells were isolated from (non-)sorted seeds before simulating digestion. The estimated lag phase describing the initial phase of starch digestion was not significantly different despite the processing intensity or the hardness category, implying that cell wall barrier properties for these samples were not majorly different. However, the rate constants and the extents of starch digestion of samples cooked for 40 min were significantly higher for the low hardness (50-65 N) compared to the high hardness (80-95 N) category (0.71 vs 1.02 starch%/min and 63 vs 77%, respectively). Kinetic evaluation of digested soluble protein (after acid hydrolysis of the digestive supernatant) showed that low hardness samples were digested faster than high hardness samples (0.037 vs 0.050 min^-1). The faster protein hydrolysis in the low hardness samples was accompanied by faster starch digestion, indicating the possible role of the protein matrix barrier. Individual cells of comparable hardness obtained from the two different processing times had similar starch and protein digestion kinetics. Our work demonstrated that, beyond cooking time, hardness is a suitable food design attribute that can be used to modulate starch and protein digestion kinetics of pulse cotyledon cells.

Proteomic Approaches to Identify Proteins Responsive to Cold Stress

Changing environmental conditions greatly affect the accumulation of many proteins; therefore, the analysis of alterations in the proteome is essential to understand the plant response to abiotic stress. Proteomics provides a platform for the identification and quantification of plant proteins responsive to cold stress and taking part in cold acclimation. Here, we describe the preparation of proteins for LC-MS measurement to monitor the changes of protein patterns during cold treatment in Arabidopsis thaliana. In our protocol, proteins are precipitated using TCA/acetone, quantified with 2D Quant Kit and digested with trypsin using a filter-based method and analyzed using an LC-MS approach. The acquired results can be further applied for label-free protein quantification.

Induction of CCK and GLP-1 release in enteroendocrine cells by egg white peptides generated during gastrointestinal digestion

The effect of dietary protein on the induction of intestinal hormones is recognised. However, little is known about the nature of the digestion products involved in this intestinal signalling. Our aim was to characterise egg white protein digestion products and study their ability to induce CCK and GLP-1 release in enteroendocrine STC-1 cells. Intestinal digests triggered GLP-1 release at a higher rate than gastric digests. Peptides, but not free amino acids, showed a potent GLP-1 secretagogue effect, while proteins only had a modest effect. CCK was released in response to peptides and free amino acids but not proteins. Two hydrophobic negatively charged peptides triggered CCK release, while the highest GLP-1 response was found with a hydrophobic positively charged peptide, pointing to the involvement of different receptors or active sites. Identifying peptide sequences and receptors involved in hormonal secretion could open up new ways to control food intake and glucose metabolism.

Dynamic gastric stability and in vitro lipid digestion of whey-protein-stabilised emulsions: Effect of heat treatment

The stability behaviours of whey-protein-stabilised emulsions under gastric conditions and the effects on the lipolysis of the emulsions were investigated using an in vitro dynamic human gastric simulator and a subsequent small intestinal model. Under gastric conditions, heated whey-protein-stabilised emulsions flocculated to a greater extent and with a larger floc size, whereas unheated emulsions were more prone to coalescence. The greater extent of flocculation delayed the delivery of oil droplets to the small intestine, leading to a lower amount of oil in the emptied gastric digesta from the heated emulsion in the early period of digestion. The differences in oil content, droplet size and interfacial composition led to a greater rate and extent of lipolysis in the subsequent intestinal digestion in the heated emulsion than the unheated emulsion. The results suggest that the lipid digestion of whey-protein-stabilised emulsions in the intestinal stage could be manipulated by thermal treatment.

The protein and peptide fractions of kashk, a traditional Middle East fermented dairy product

Kashk is a typical dairy product of Iran, made from sour milk. It is traditionally produced from buttermilk in a dry, round-shaped form. Today, it is also produced at industrial level in a liquid form starting from fermented milk. We aimed to characterise the kashk proteome and peptidome comparing a traditional product with the industrial using a combination of proteomic approaches including advanced chromatographic and electrophoretic separation technique coupled to tandem mass spectrometry. We identified also phosphorylated casein-derived peptides (CPP) and investigated kashk protein digestibility using a static model of food protein digestion. The molecular characterization, coupled with bioinformatic in silico analysis, allowed the identification of potential bioactive peptides.

A novel type 1 cystatin involved in the regulation of Rhipicephalus microplus midgut cysteine proteases

Rhipicephalus microplus is a cattle ectoparasite found in tropical and subtropical regions around the world with great impact on livestock production. R. microplus can also harbor pathogens, such as Babesia sp. and Anaplasma sp. which further compromise cattle production. Blood meal acquisition and digestion are key steps for tick development. In ticks, digestion takes place inside midgut cells and is mediated by aspartic and cysteine peptidases and, therefore, regulated by their inhibitors. Cystatins are a family of cysteine peptidases inhibitors found in several organisms and have been associated in ticks with blood acquisition, blood digestion, modulation of host immune response and tick immunity. In this work, we characterized a novel R. microplus type 1 cystatin, named Rmcystatin-1b. The inhibitor transcripts were found to be highly expressed in the midgut of partially and fully engorged females and they appear to be modulated at different days post-detachment. Purified recombinant Rmcystatin-1b displayed inhibitory activity towards typical cysteine peptidases with high affinity. Moreover, rRmcystatin-1b was able to inhibit native R. microplus cysteine peptidases and RNAi-mediated knockdown of the cystatin transcripts resulted in increased proteolytic activity. Moreover, rRmcystatin-1b was able to interfere with B. bovis growth in vitro. Taken together our data strongly suggest that Rmcystatin-1b is a regulator of blood digestion in R. microplus midgut.

Comparative peptidomic profile and bioactivities of cooked beef, pork, chicken and turkey meat after in vitro gastro-intestinal digestion

This study was designed to investigate the potential contribution of bioactive peptides to the biological activities related to the consumption of pork, beef, chicken and turkey meat following in vitro gastro-intestinal digestion. After extraction of the peptidic fractions from digested samples, the bioactivities were evaluated by in vitro antioxidant activity as well as angiotensin-converting enzyme (ACE) and dipeptidyl peptidase-IV (DPP-IV) inhibition assays. Pork and turkey meat appeared to be the best sources of antioxidant peptides. Pork was found to be the best source of DPP-IV-inhibitory peptides whereas chicken meat supplied peptides with the highest ACE-inhibitory activity. The comprehensive analysis of the peptidomic profile of digested samples was performed by nano-LC-ESI-QTOF MS/MS analysis. A total of 217, 214, 257 and 248 peptides were identified in digested pork, beef, chicken and turkey meat, respectively. Chicken and turkey meat showed the highest similarity in peptide sequences with 202 common peptides. Sixty-two peptides matched with sequences with previously demonstrated biological activity. In particular, 35 peptides showed ACE-inhibitory activity and 23 DPP-IV inhibitory activity. Twenty-two bioactive peptides were commonly released from the different types of meat. The relative amount of identified bioactive peptides were positively correlated to the biological activities of the different digested meats. BIOLOGICAL SIGNIFICANCE: The present study describes for the first time a comprehensive peptide profile of four types of meat after in vitro gastro-intestinal digestion. The peptide inventory was used to identify 62 bioactive peptides with ACE- and DPPIV-inhibitory and antioxidant activities. The bioactivity analysis revealed interesting and significant differences between the studied meats. The originality of this work lay in the description of intrinsic differences in physiological functions after the ingestion of meat proteins from different species. In a context in which the current research scene relates meat consumption to the onset of chronic pathologies, this peptide profiling and bioactivity analysis shed light on the possible health benefits of peptides released from meat proteins. In fact, this paper represents a sort of detailed peptide list that may help to predict which peptides could be generated after meat intake and detectable at gastro-intestinal level. It also provides a thorough investigation of novel biological activities associated to meat protein hydrolysates, giving a new positive aspect to meat consumption.

A Standardized and Reproducible Proteomics Protocol for Bottom-Up Quantitative Analysis of Protein Samples Using SP3 and Mass Spectrometry

The broad utility of mass spectrometry (MS) for investigating the proteomes of a diverse array of sample types has significantly expanded the use of this technology in biological studies. This widespread use has resulted in a substantial collection of protocols and acquisition approaches designed to obtain the highest-quality data for each experiment. As a result, distilling this information to develop a standard operating protocol for essential workflows, such as bottom-up quantitative shotgun whole proteome analysis, can be complex for users new to MS technology. Further complicating this matter, in-depth description of the methodological choices is seldom given in the literature. In this work, we describe a workflow for quantitative whole proteome analysis that is suitable for biomarker discovery, giving detailed consideration to important stages, including (1) cell lysis and protein cleanup using SP3 paramagnetic beads, (2) quantitative labeling, (3) offline peptide fractionation, (4) MS analysis, and (5) data analysis and interpretation. Special attention is paid to providing comprehensive details for all stages of this proteomics workflow to enhance transferability to external labs. The standardized protocol described here will provide a simplified resource to the proteomics community toward efficient adaptation of MS technology in proteomics studies.

Peptidomic profiling of human milk with LC-MS/MS reveals pH-specific proteolysis of milk proteins

Human milk is a dynamic protein-protease system that delivers bioactive peptides to infants. The pH of milk changes from the mother's mammary gland to the infant's digestive tract. Although the release of human milk peptides has been studied during in vivo or in vitro digestion, these models did not explicitly vary nor observe the effect of pH. The objective of this research was to determine the effect of pH on the proteolysis of human milk. Using high-resolution accurate-mass Orbitrap mass spectrometry, profiles of endogenous human milk peptides before and after incubation at various pH levels have been mapped. Over 5000 peptides were identified. Comparative analyses classified 74 peptides that were consistently found independent of pH alterations, and 8 peptides that were released only at pH 4 or 5 (typical infant gastric pH). Results documented that the proteolysis of milk proteins, particularly β-casein, polymeric immunoglobulin receptor, and α-lactalbumin, is pH-dependent.

Stability of allergens

For proteins to cause IgE-mediated allergic reactions, several common characteristics have to be defined, including small molecular size, solubility and stability to changing pH levels and enzymatic degradation. Nevertheless, these features are not unique for potent allergens, but are also observed in non-allergenic proteins. Due to the increasing awareness by regulatory authorities regarding the allergy pandemic, definition of characteristics unique to potent allergens would facilitate allergenicity assessment in the future. Despite major research efforts even to date the features unique for major allergens have not been elucidated so far. The route of allergen entry into the organism determines to a great extent these required characteristics. Especially orally ingested allergens are exposed to the harsh milieu of the gastrointestinal tract but might additionally be influenced by food processing. Depending on molecular properties such as disulphide bonds contributing to protein fold and formation of conformational IgE epitopes, posttranslational protein modification or protein food matrix interactions, enzymatic and thermal stability might differ between allergens. Moreover, also ligand binding influences structural stability. In the current review article, we aim at highlighting specific characteristics and molecular pattern contributing to a stabilized protein structure and overall allergenicity.

A novel protein digestion method with the assistance of alternating current denaturation for high efficient protein digestion and mass spectrometry analysis

Protein denaturation has always displayed a huge necessity for mass spectrometry (MS)-based protein identification methods in proteomics. In this research, a novel protein digestion method with the assistance of alternating current (AC) denaturation has been proposed and evaluated. In this method, merely, 200 mM ammonium bicarbonate buffer solution (pH, 8.2) was used to dissolve proteins and act as the electrolyte, and protein denaturation could be achieved in several seconds. For apo-transferrin, ovalbumin and bovine serum albumin that are resistant to digestion in their native states, confident amino acid sequence coverage by matrix assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis were obtained after 200 v AC denaturation. The applicability of this method was further investigated via analyzing a rat liver proteome sample using nano reversed phase liquid chromatography-electrospray ionization-tandem mass spectrometry (nanoRPLC-ESI-MS/MS). As a result, 458 proteins were identified which is comparable to the in-solution digestion via 8 M urea denaturation (375 proteins). All these results demonstrated that AC denaturation could offer an efficient assistance for a clean and high-throughput digestion in the individual level and proteome level.

Protein Digestion for DIGE Analysis

In-gel digestion of protein spots derived from two-dimensional gels and their subsequent identification by mass spectrometry is involved in a multitude of mass spectrometry-driven proteomic experiments, including fluorescence difference gel electrophoresis (DIGE). This type of proteomic methodology has been involved in the establishment of comparative proteome maps and in the identification of differentially expressed proteins and protein isoforms in health and disease. Most in-gel digestion protocols follow a number of common steps including excision of the protein spots of interest, de-staining, reduction and alkylation (for silver-stained gels), dehydration and overnight digestion with the proteolytic enzyme of choice. While trypsin has been a mainstay of peptide digestion for many years, it does have its shortcomings, particularly related to incomplete peptide digestion, and this has led to a rise in popularity for other proteolytic enzymes either used alone or in combination. This chapter discusses the alternative enzymes available and describes the process of in-gel digestion using the enzyme trypsin.

Filter-Aided Sample Preparation for Proteome Analysis

Quantitative protein extraction and high-yield generation of peptides from biological samples are the prerequisite for successful bottom-up type proteomic analysis. Filter aided sample preparation (FASP) is a method for processing of SDS-solubilized cells in a proteomic reactor format. In FASP, disposable centrifugal ultrafiltration units allow for detergent depletion, protein digestion, and isolation of peptides released by proteases from undigested material. Consecutive protein digestion with two or three proteases enables generation of peptide fractions with minimal overlap and considerably increases the number of identifications and protein sequence coverage. FASP is useful for analysis of samples varying in size from a few micrograms to several milligrams of total protein.

Data on the chemical properties of commercial fish sauce products

This data article reports on the chemical properties of commercial fish sauce products associated with the fish sauce taste and flavor. All products were analyzed in triplicate. Dried solid content was analyzed by moisture analyzer. Fish sauce salinity was determined by a salt meter. pH was measured using a pH meter. The acidity was determined using a titration assay. Amino nitrogen and total nitrogen were evaluated using a titration assay and Combustion-type nitrogen analyzer, respectively. The analyzed products originated from Japan, Thailand, Vietnam, China, the Philippines, and Italy. Data on the chemical properties of the products are provided in table format in the current article.

Comparative Testis Tissue Proteomics Using 2-Dye Versus 3-Dye DIGE Analysis

Comparative tissue proteomics aims to analyze alterations of the proteome in response to a stimulus. Two-dimensional difference gel electrophoresis (2D-DIGE) is a modified and advanced form of 2D gel electrophoresis. DIGE is a powerful biochemical method that compares two or three protein samples on the same analytical gel, and can be used to establish differentially expressed protein levels between healthy normal and diseased pathological tissue sample groups. Minimal DIGE labeling can be used via a 2-dye system with Cy3 and Cy5 or a 3-dye system with Cy2, Cy3, and Cy5 to fluorescently label samples with CyDye flours pre-electrophoresis. DIGE circumvents gel-to-gel variability by multiplexing samples to a single gel and through the use of a pooled internal standard for normalization. This form of quantitative high-resolution proteomics facilitates the comparative analysis and evaluation of tissue protein compositions. Comparing tissue groups under different conditions is crucially important for advancing the biomedical field by characterization of cellular processes, understanding pathophysiological development and tissue biomarker discovery. This chapter discusses 2D-DIGE as a comparative tissue proteomic technique and describes in detail the experimental steps required for comparative proteomic analysis employing both options of 2-dye and 3-dye DIGE minimal labeling.

Preparation and characterization of a packed bead immobilized trypsin reactor integrated into a PDMS microfluidic chip for rapid protein digestion

This paper demonstrates the design, efficiency and applicability of a simple, inexpensive and high sample throughput microchip immobilized enzymatic reactor (IMER) for rapid protein digestion. The IMER contains conventional silica particles with covalently immobilized trypsin packed inside of a poly(dimethylsiloxane) (PDMS) microchip channel (10mm×1mm×35µm). The microchip consists of 9 different channels, enabling 9 simultaneous protein digestions. Trypsin was covalently immobilized using carbodiimide activation, the ideal trypsin/silica particle ratio (i.e. measured mass ratio before the immobilization reaction) was determined. The amount of immobilized trypsin was 10-15μg trypsin for 1mg silica particle. Migration times of CZE peptide maps showed good repeatability and reproducibility (RSD%=0.02-0.31%). The IMER maintained its activity for 2 months, in this period it was used effectively for rapid proteolysis. Four proteins (myoglobin, lysozyme, hemoglobin and albumin) in a wide size range (15-70kDa) were digested to demonstrate the applicability of the reactor. Their CZE peptide maps were compared to peptide maps obtained from standard in-solution digestion of the four proteins. The number of peptide peaks correlated well with the theoretically expected peptide number in both cases, the peak patterns of the electropherograms were similar, however, digestion with the microchip IMER requires only <10s, while in-solution digestion takes 16h. LC-MS/MS peptide mapping was also carried out, the four proteins were identified with satisfying sequence coverages (29-50%), trypsin autolysis peptides were not detected. The protein content of human serum was digested with the IMER and with in-solution digestion.

3D-SISPROT: A simple and integrated spintip-based protein digestion and three-dimensional peptide fractionation technology for deep proteome profiling

Multidimensional peptide fractionation strategies have been approved as the efficient approaches to significantly improve the depth of proteome coverage. In this study, a simple and integrated spintip-based protein digestion and three-dimensional peptide fractionation technology (3D-SISPROT) was developed for the deep proteome profiling from low microgram of proteins as starting materials. All the sample preparation steps, including protein digestion, strong anion exchange (SAX)-based fractionation, and high-pH reversed phase (RP) fractionation were integrated into one pipette tip packed with SAX and C₁₈ membranes for the first time. The SAX plus C₁₈ membranes design minimizes the sample loss and ensures high efficient SAX-based digestion. 4275 proteins were identified with 1.4h of MS time when 6μg cell lysates was processed. More importantly, the SAX-based digestion procedure did not influence the SAX-based peptide fractionation efficiency which was done in the same SAX membrane. The 3D-SISPROT was exemplified by the analysis of 30μg of HEK 293T cell lysates with 20.4h of MS time, which resulted in the identification of 8222 proteins including 3215 annotated membrane proteins. Gene Ontology annotations indicated that the 3D-SISPROT was unbiased for the proteins from major cellular components. Taking advantages of the efficient SAX-based and high-pH RP-based fractionation strategies, we expect that the 3D-SISPROT can be applied for the deep proteome profiling with limited starting material.

Clinical Proteomics: Liquid Chromatography-Mass Spectrometry (LC-MS) Purification Systems

Liquid chromatography-mass spectrometry (LC-MS) has become a routine powerful technology in clinical proteomic studies for protein identification, protein characterization and the discovery of biomarkers. In this chapter, we describe two protocol methods to analyze clinical patient samples using a resin based depletion column followed by either protein In-gel enzymatic digestion or protein in-solution enzymatic digestion and then analysis by one-dimensional reverse-phase chromatography or two-dimensional strong cation exchange (SCX)-reverse-phase chromatography (RPC).

High-Throughput Parallel Proteomic Sample Preparation Using 96-Well Polyvinylidene Fluoride (PVDF) Membranes and C18 Purification Plates

Meaningful proteomic-based biomarker discovery projects using primary human-derived specimens require the analysis of hundreds of samples in order to address the issue of interpersonal variability. Thus, robust high-throughput methods for the digestion of plasma samples are a prerequisite for such large clinical proteomic studies with hundreds of samples. Commonly used sample preparation methods are often difficult to parallelize and/or automate. Herein we describe a method for parallel 96-well plate-based sample preparation. Protein digestion is performed in 96-well polyvinylidene fluoride (PVDF) membrane plates and the subsequent purification in 96-well reversed phase C18 purification plates, enabling the usage of multichannel pipettes in all steps. The protocol can be applied using neat or depleted plasma/serum samples, but has also proven effective with other sample types.

Di- and tripeptide transport in vertebrates: the contribution of teleost fish models

Solute Carrier 15 (SLC15) family, alias H⁺-coupled oligopeptide cotransporter family, is a group of membrane transporters known for their role in the cellular uptake of di- and tripeptides (di/tripeptides) and peptide-like molecules. Of its members, SLC15A1 (PEPT1) chiefly mediates intestinal absorption of luminal di/tripeptides from dietary protein digestion, while SLC15A2 (PEPT2) mainly allows renal tubular reabsorption of di/tripeptides from ultrafiltration, SLC15A3 (PHT2) and SLC15A4 (PHT1) possibly interact with di/tripeptides and histidine in certain immune cells, and SLC15A5 has unknown function. Our understanding of this family in vertebrates has steadily increased, also due to the surge of genomic-to-functional information from 'non-conventional' animal models, livestock, poultry, and aquaculture fish species. Here, we review the literature on the SLC15 transporters in teleost fish with emphasis on SLC15A1 (PEPT1), one of the solute carriers better studied amongst teleost fish because of its relevance in animal nutrition. We report on the operativity of the transporter, the molecular diversity, and multiplicity of structural-functional solutions of the teleost fish orthologs with respect to higher vertebrates, its relevance at the intersection of the alimentary and osmoregulative functions of the gut, its response under various physiological states and dietary solicitations, and its possible involvement in examples of total body plasticity, such as growth and compensatory growth. By a comparative approach, we also review the few studies in teleost fish on SLC15A2 (PEPT2), SLC15A4 (PHT1), and SLC15A3 (PHT2). By representing the contribution of teleost fish to the knowledge of the physiology of di/tripeptide transport and transporters, we aim to fill the gap between higher and lower vertebrates.

Studying the effect of microwave heating on the digestion process and identification of proteins

The impact of microwave irradiation on the in-solution digestion processes and the detection limit of proteins are systematically studied. Kinetic processes of many peptides produced through the trypsin digestion of various proteins under microwave heating at 50°C were investigated with MALDI-MS. This study also examines the detection limits and digestion completeness of individual proteins under microwave heating at 50°C and at different time intervals (1, 5 and 30 min) using LC-MS. We conclude that if the peptides without missed cleavage dictate the detection limit, conventional digestion will lead to a better detection limit. The detection limit may not differ between the microwave and conventional heating if the peptides with missed cleavage sites and strong intensity are formed at the very early stage (i.e., less than 1 min) and are not further digested throughout the entire digestion process. The digestion of Escherichia coli lysate was compared under conventional and short time (microwave) conditions. The number of proteins identified under conventional heating exceeded that obtained from microwave heating over heating periods less than 5 min. The overall results show that the microwave-assisted digestion is not complete. Although the sequence coverage might be better, the detection limit might be worse than that under conventional heating.

A novel protocol for enzymatic digestion based on covalent binding by protein immobilization

The process of protein digestion is a critical step for successful protein identification in proteomic analysis. Many efforts have been dedicated to enhancing the digestion efficiency for sufficient digestion. Among these approaches, protein complete denaturation with denaturants is a common process for better digestion. However, the removal of denaturants was tedious or would cause protein loss and other problems. In this work, a feasible digestion approach, immobilized protein digestion (IPD), based on covalent binding has been developed. Proteins can be completely denatured and immobilized on the surface of functional materials by covalent binding to form a monolayer. Subsequently, varieties of denaturants or contaminants would be removed thoroughly by washing. To achieve fast immobilization and high digestion efficiency, different functional materials and denaturants were selected. Compared with traditional in-solution digestion, the method achieved a prominent increase in identified peptides numbers and sequence coverage of proteins. Data analysis also showed that covalent binding could evidently decrease enzymatic missed cleavage for various protein sequences. Furthermore, possible peptide losses due to covalent binding were also investigated. Also, it has been proved to be efficient for complex biological sample digestion. Graphical abstract Workflow of the IPD method, including protein denaturation, immobilization, digestion, and identification.

Simulated GI digestion of dietary protein: Release of new bioactive peptides involved in gut hormone secretion

Dietary proteins have been reported to induce a strong feeling of satiety that has been partially explained by gut hormone level increase. Up to date, various protein hydrolysates have demonstrated in vitro and in vivo their potential to stimulate gut hormone secretion related to food intake decrease and their mechanisms of action have just started to be resolved. In this context, this study aimed at identifying new peptide sequences involved in gut hormone secretion released by protein in vitro gastrointestinal digestion. Targeted gut hormones were Cholecystokinin (CCK) and Glucagon-Like Peptide 1 (GLP-1). The activity of DPP-IV was also considered as it strongly modulates GLP-1 action. In a previous study, simulated digestion of dietary protein has generated hydrolysates with enhancing effect on CCK and GLP-1 secretion in STC-1 cells as well as DPP-IV inhibitory properties. Successive purification steps were performed to isolate peptide fractions involved in these bioactivities whose sequence was determined by LC-MS-MS. Three peptide sequences ANVST, TKAVEH and KAAVT were pointed out for their stimulating effects on GLP-1 secretion. The sequence VAAA was isolated for its DPP-IV inhibitory properties. Two peptide groups were strongly involved in CCK release sharing a certain occurrence of aromatic amino acid residues.