Enzymatic Digestion Of Proteins Research Articles

Perilla peptides delay the progression of kidney disease by improving kidney apoptotic injury and oxidative stress and maintaining intestinal barrier function

Chronic kidney disease has become one of the most threatening diseases to human health worldwide. Kidney lesions can lead to a series of diseases such as damage to other organs and elevated blood lipids. In this study, perilla peptide, a small molecule peptide prepared by enzymatic digestion of perilla protein, ameliorated adenine-induced apoptotic kidney injury and oxidative stress, attenuated organ inflammatory response, and improved kidney injury status. In addition, perilla peptides maintained the integrity of intestinal barrier function in mice, increased the expression of intestinal tight junction proteins, and reduced the multiplication of multiple pathogenic bacteria in the intestine, thus reducing the accumulation of endotoxins in the blood. In conclusion, this study demonstrated that perilla peptides have positive ameliorative effects in kidney diseases and have potential applications in the development of functional foods.

Proteomics reveals commitment to germination in barley seeds is marked by loss of stress response proteins and mobilisation of nutrient reservoirs

Germination is a critical process in the reproduction and propagation of flowering plants, and is also the key stage of industrial grain malting. Germination commences when seeds are steeped in water, followed by degradation of the endosperm cell walls, enzymatic digestion of starch and proteins to provide nutrients for the growing plant, and emergence of the radicle from the seed. Dormancy is a state where seeds fail to germinate upon steeping, but which prevents inappropriate premature germination of the seeds before harvest from the field. This can result in inefficiencies in industrial malting. We used Sequential Window Acquisition of all THeoretical ions Mass Spectrometry (SWATH-MS) proteomics to measure changes in the barley seed proteome throughout germination. We found a large number of proteins involved in desiccation tolerance and germination inhibition rapidly decreased in abundance after imbibition. This was followed by a decrease in proteins involved in lipid, protein and nutrient reservoir storage, consistent with induction and activation of systems for nutrient mobilisation to provide nutrients to the growing embryo. Dormant seeds that failed to germinate showed substantial biochemical activity distinct from that of seeds undergoing germination, with differences in sulfur metabolic enzymes, endogenous alpha-amylase/trypsin inhibitors, and histone proteins. We verified our findings with analysis of germinating barley seeds from two commercial malting facilities, demonstrating that key features of the dynamic proteome of germinating barley seeds were conserved between laboratory and industrial scales. The results provide a more detailed understanding of the changes in the barley proteome during germination and give possible target proteins for testing or to inform selective breeding to enhance germination or control dormancy. SignificanceGermination is critical to the reproduction and propagation of flowering plants, and in industrial malting. Dormancy, where seeds fail to germinate upon steeping, can result in inefficiencies in industrial malting. Our DIA/SWATH-MS proteomics analyses identified key changes during germination, including an initial loss of proteins involved in desiccation tolerance and germination inhibition, followed by decreases in lipid, protein and nutrient reservoir storage. These changes were consistent between laboratory and industrial malting scales, and therefore demonstrate the utility of laboratory-scale barley germination as a model system for industrial malt house processes. We also showed that dormant seeds that failed to germinate showed substantial biochemical activity distinct from that of seeds undergoing germination, consistent with dormancy being an actively regulated state. Our results provide a more detailed understanding of the changes in the barley proteome during germination and give possible target proteins for testing or to inform selective breeding to enhance germination or control dormancy.

Proteomics of Human Milk: Definition of a Discovery Workflow for Clinical Research Studies.

Milk is a complex biological fluid composed mainly of water, carbohydrates, lipids, proteins, and diverse bioactive factors. Human milk represents a unique tailored source of nutrients that adapts during lactation to the specific needs of the developing infant. Proteins in milk have been studied for decades, and proteomics, peptidomics, and glycoproteomics are the main approaches previously deployed to decipher the proteome of human milk. In the present work, we aimed at implementing a highly automated pipeline for the proteomic analysis of human milk with liquid chromatography mass spectrometry (MS). Commercial human milk samples were used to evaluate and optimize workflows. Centrifugation for defatting milk samples was assessed before and after reduction, alkylation, and enzymatic digestion of proteins, without and with presence of surfactants. Skimmed milk samples were analyzed using isobaric labeling-based quantitative MS on an Orbitrap Tribrid mass spectrometer. Sample fractionation using isoelectric focusing was also evaluated to more deeply profile the human milk proteome. Finally, the most appropriate workflow was transferred to a liquid handling workstation for automated sample preparation. In conclusion, we have defined and describe herein an efficient highly automated proteomic workflow for human milk sample analysis. It is compatible with clinical research, possibly allowing the analysis of sufficiently large cohorts of samples.

Enrichment of Intact Glycopeptides Using Strong Anion Exchange and Electrostatic Repulsion Hydrophilic Interaction Chromatography.

Glycosylation is a biologically important and complex protein posttranslational modification. The emergence of glycoproteomic technologies to identify and characterize glycans on proteins has the potential to enable a better understanding the role of glycosylation in biology, disease states, and other areas of interest. In particular, the analysis of intact glycopeptides by mass spectrometry allows information about glycan location and composition to be ascertained. However, such analysis is often complicated by extensive glycan diversity and the low abundance of glycopeptides in a complex mixture relative to nonglycosylated peptides. Enrichment of glycopeptides from a protein enzymatic digest is an effective approach to overcome such challenges. In this chapter, we described a glycopeptide enrichment method combining strong anion exchange, electrostatic repulsion, and hydrophilic interaction chromatography (SAX-ERLIC). Following enzymatic digestion of proteins into peptides, SAX-ERLIC is performed by solid phase extraction to enrich glycopeptides from biological samples with subsequent LC-MS/MS analysis. Glycopeptide data generated using the SAX-ERLIC enrichment yields a high number of total and unique glycopeptide identifications which can be mapped back to proteins. The enrichment strategy is robust, easy to perform, and does not require cleavage of glycans prior to LC-MS/MS analysis.

Software Options for the Analysis of MS-Proteomic Data.

Mass spectrometry (MS)-based proteomics is currently the most successful approach to measure and compare peptides and proteins in a large variety of biological samples. Modern mass spectrometers, equipped with high-resolution analyzers, provide large amounts of data output. This is the case of shotgun/bottom-up proteomics, which consists in the enzymatic digestion of protein into peptides that are then measured by MS-instruments through a data dependent acquisition (DDA) mode. Dedicated bioinformatic tools and platforms have been developed to face the increasing size and complexity of raw MS data that need to be processed and interpreted for large-scale protein identification and quantification. This chapter illustrates the most popular bioinformatics solution for the analysis of shotgun MS-proteomics data. A general description will be provided on the data preprocessing options and the different search engines available, including practical suggestions on how to optimize the parameters for peptide search, based on hands-on experience.

Biofilm formation by ST17 and ST19 strains of Streptococcus agalactiae

Bacterial biofilms are an important virulence factor with a vital role in evasion from the host immune system, colonization and infection. The aim of the present study was to evaluate in vitro the effects of three environmental factors (H+, glucose and human plasma) in biofilm formation, by carrier and invasive Streptococcus agalactiae strains of ST17 and ST19 sequence types, including DNase producers and non-producers. Bacteria ability to assemble biofilms was classified based on crystal violet assay. Biofilm formation was also monitored by scanning electron microscopy. Depending on the growth medium used, each bacterial isolate could fit in different biofilm production categories. Our data showed that optimal conditions for S. agalactiae biofilm assembly were reached after 48 h incubation at pH 7.6 in the presence of glucose and inactivated human plasma. In the presence of inactivated human plasma, the biofilm biomass of ST19 strains experienced a higher increase than ST17 strains. The composition of the extracellular polymeric matrix of the three strongest biofilm producers (all from ST17) was accessed by enzymatic digestion of mature biofilms and proteins were shown to be the predominant component. The detailed identification of the extracellular protein components should contribute to the development of new therapeutic strategies to fight S. agalactiae infections.

Fluorescence correlation spectroscopy as a tool to investigate the directionality of proteolysis

Enzymatic proteolysis or protein digestion is the fragmentation of protein into smaller peptide units under the action of peptidase enzymes. In this contribution, the directionality of proteolysis has been studied using fluorescence correlation spectroscopy (FCS), taking human serum albumin (HSA) as the model protein and papain, chymotrypsin and trypsin as the model enzymes. Domain-I of HSA has been tagged with tetramethylrhodamine-5-maleimide (TMR) and domain-III with p-nitrophenylcoumarin ester (NPCE) separately and subjected to proteolysis. Following the change in hydrodynamic radius, as monitored by FCS, it has been confirmed that under similar experimental conditions the order of efficiency of digestion is papain > trypsin > chymotrypsin. More interestingly, a faster decrease of hydrodynamic radius was observed when the fluorescence from domain-I was monitored in FCS, compared to that of domain-III. This observation clearly indicates that all these enzymes prefer to start cleaving HSA from domain-I. We assign this preference to the hydrophilic natures of the enzyme active site and domain-I surface. The dependence of the proteolysis on temperature and enzyme concentration has also been studied for papain using the same approach. Reverse-phase HPLC results are found to be in line with the FCS results and validates the applicability of our proposed method.

Boosting Auto-Induction of Recombinant Proteins in Escherichia coli with Glucose and Lactose Additives.

BackgroundAuto-induction is a convenient way to produce recombinant proteins without inducer addition using lac operon-controlled Escherichia coli expression systems. Auto-induction can occur unintentionally using a complex culture medium prepared by mixing culture substrates. The differences in culture substrates sometimes lead to variations in the induction level.ObjectivesIn this study, we investigated the feasibility of using glucose and lactose as boosters of auto-induction with a complex culture medium.MethodsFirst, auto-induction levels were assessed by quantifying recombinant GFPuv expression under the control of the T7 lac promoter. Effectiveness of the additive-containing medium was examined using ovine angiotensinogen (tac promoter-based expression) and Thermus thermophilus manganese-catalase (T7 lac promoter-based expression).ResultsAuto-induced GFPuv expression was observed with the enzymatic protein digest Polypepton, but not with another digest tryptone. Regardless of the type of protein digest, supplementing Terrific Broth medium with glucose (at a final concentration of 2.9 g/L) and lactose (at a final concentration of 7.6 g/L) was successful in obtaining an induction level similar to that achieved with a commercially available auto-induction medium. The two recombinant proteins were produced in milligram quantity of purified protein per liter of culture.ConclusionThe medium composition shown in this study would be practically useful for attaining reliable auto-induction for E. coli-based recombinant protein production.

A Novel Combined Microstrip Resonator/Nanospray Ionization Source for Microwave-Assisted Trypsin Digestion of Proteins.

Enzymatic digestion of proteins is a critical step in bottom-up and middle-down proteomics. Here, we demonstrate a method for decreasing the time required for proteolytic digestion of proteins from multiple hours to minutes by using an in-line microstrip cavity for programmed microwave heating. When a nanospray emitter tip, containing a digestion sample, is exposed to a region of highly focused microwave field, the rate of proteolytic digestion is enhanced and the time required for digestion greatly decreased. The design is advantageous for mass spectrometry because the solution-based digestion can then be directly sprayed from a nanoelectrospray tip emitter, decreasing sample transfer loss and allowing the system to be used in a flow-through proteolytic workflow. Microwave-assisted digestion using this method is evaluated against standard overnight digestion protocols using a variety of proteins, evaluating sequence coverage and observed peptide location, digestion rate, and overall efficacy. The influence of applied microwave power is investigated, and enzymatic kinetic parameters are evaluated to estimate temperature within the microreactor. Finally, the modulation of the proteolytic digestion of proteins based upon the modulation of applied microwave power is demonstrated on a time scale of seconds in a flow-through system.

Ultrafast enzymatic digestion of proteins by microdroplet mass spectrometry

Enzymatic digestion for protein sequencing usually requires much time, and does not always result in high sequence coverage. Here we report the use of aqueous microdroplets to accelerate enzymatic reactions and, in particular, to improve protein sequencing. When a room temperature aqueous solution containing 10 µM myoglobin and 5 µg mL−1 trypsin is electrosonically sprayed (−3 kV) from a homemade setup to produce tiny (∼9 µm) microdroplets, we obtain 100% sequence coverage in less than 1 ms of digestion time, in sharp contrast to 60% coverage achieved by incubating the same solution at 37 °C for 14 h followed by analysis with a commercial electrospray ionization source that produces larger (∼60 µm) droplets. We also confirm the sequence of the therapeutic antibody trastuzumab (∼148 kDa), with a sequence coverage of 100% for light chains and 85% for heavy chains, demonstrating the practical utility of microdroplets in drug development.

Proteomics of arthropod soluble olfactory proteins.

Shotgun proteomics is a very sensitive bottom-up approach used to study complex mixtures of proteins through a combination of high-performance liquid chromatography (HPLC) and high-resolution mass spectrometry (HRMS). This technique has been successfully applied to the study of olfactory appendixes of insects and other arthropods. Since extracting soluble proteins from tissues and processing them for shotgun proteomics is quite straightforward, the technique has proved to be very suitable for studying soluble olfactory proteins, such as odorant binding proteins (OBPs), chemosensory proteins (CSPs) and Niemann-Pick type 2 proteins. Here, we describe the main principles and methods at the basis of shotgun proteomics, including its use to quantify proteins through label-free quantification. We also provide operational protocols for the experimental workflow steps, i.e., insect dissection, protein extraction, protein enzymatic digestion, sample purification, HPLC-MS analysis, search of mass spectral data against polypeptide databases and first steps in the analysis of the search results.

Improving the throughput of immunoaffinity purification and enzymatic digestion of therapeutic proteins using membrane-immobilized reagent technology

Continued interest in protein therapeutics has motivated the development of improved bioanalytical tools to support development programs. LC-MS offers specificity, sensitivity, and multiplexing capabilities without the need for target-specific reagents, making it a valuable alternative to ligand binding assays. Immunoaffinity purification (IP) and enzymatic digestion are critical, yet extensive and time-consuming components of the "gold standard" bottom-up approach to LC-MS-based protein quantitation. In the present work, commercially available technology, based on membrane-immobilized reagents in spin column and plate format, is applied to reduce IP and digestion times from hours to minutes. For a standard monoclonal antibody, the lower limit of quantitation was 0.1 ng μL-1 compared to 0.05 ng μL-1 for the standard method. A pharmacokinetics (PK) study dosing Herceptin in rat was analyzed by both the membrane and the standard method with a total sample processing time of 4 h and 20 h, respectively. The calculated concentrations at each time point agreed within 8% between both methods, and PK values including area under the curve (AUC), half-life (T1/2), mean residence time (MRT), clearance (CL), and volume of distribution (Vdss) agreed within 6% underscoring the utility of the membrane methodology for quantitative bioanalysis workflows.

Quadrupole-Time-of-Flight Mass Spectrometric Identification of Hemoglobin Subunits α, β, γ and δ in Unknown Peaks of High Performance Liquid Chromatography of Hemoglobin in β-Thalassemias

This is the first report of quadrupole time-of-flight (Q-TOF) mass spectrometric identification of the hemoglobin (Hb) subunits, α, β, δ and γ peptides, derived from enzymatic-digestion of proteins in the early unknown peaks of the cation exchange chromatography of Hb. The objectives were to identify the unknown high performance liquid chromatography (HPLC) peaks in healthy subjects and in patients with β-thalassemia (β-thal). The results demonstrate the existence of pools of free globin chains in red blood cells (RBCs). The α-, β-, δ- and γ-globin peptides were identified in the unknown HPLC peaks. The quantification and role of the free globin pool in patients with β-thal requires further investigation. Identification of all types of Hb subunits in the retention time (RT) before 1 min. suggests that altered Hbs is the nature of these fast-eluting peaks. Relevancy of thalassemias to the protein-aggregation disorders will require review of the role of free globin in the pathology of the disease.

Relative proteome quantification of alpha, beta, gamma and delta globin chains in early eluting peaks of Bio-Rad variant II® CE-HPLC of hemoglobin from healthy and beta-thalassemia subjects in Malaysia

This is the first report of QQQ-mass spectrometric identification and quantification of the Hb subunits, alpha, beta, delta and gamma globin peptides, derived from enzymatic-digestion of proteins in the early unknown peaks of the Bio-Rad cation-exchange chromatography of haemoglobin. The objectives were to assess the relationship of the quantity of the free alpha, beta, delta and gamma globin chains with the phenotypic diversity of beta-thalassaemias (β-thal). The results demonstrate that the pools of free globin chains in red blood cells were correlating with the severity of the disease in patients with different phenotypes of β-thal. The mechanism and the regulation of synthesis of free globin chains pool in a normal individual and in patients with different β-thal phenotypes could arise from several mechanisms which will require further investigation. The role of the free globin pool in patients with β-thal for development of novel therapeutic approaches based on these potential targets requires further investigation. Pertinent biomarkers improves the diagnosis of the β-thal, especially in low-income countries where they are most common and allows more effective therapeutic intervention leading to more successful therapeutic outcome.

Gastro-intestinal Digestibility of Processed Forms of Cow’s Milk Proteins under Simulated Infant and Adult Conditions Characterised by in vitro Methods

Human digestion involves chemical, biochemical and fermentative processes integrated to achieve optimal nutrient absorption along the gastro-intestinal (GI) tract. In particular, efficient gastro-intestinal enzymatic digestion of proteins is critical for maximum upper intestinal protein absorption and may influence the distribution of dietary protein between the ‘host’ and microbiota. However, the relative efficiency of infant versus adult conditions of GI digestion of cow’s milk products have not been systematically studied. Conditions for in vitro GI enzymatic digestion, optimised for either infant or adult conditions, were applied to test pasteurised, skimmed milk, skimmed milk powder (SMP) and whey and casein protein fractions of cow’s milk. Research methods included digestion monitoring by o-phthaldialdehyde (OPA) derivitisation of peptides and free amino acids, and digestate analysis to characterise low mass ‘absorbing’ products (size exclusion chromatography) and larger non-absorbing products (700-3500 Da) by MALDI-TOF-MS. The results demonstrated significantly lower digestion efficiency for infant versus adult digestion conditions, particularly in the gastric phase. Digestibility of pasteurised milk and SMP were generally lower than either whey or casein protein fractions. Lower overall protein digestibility was associated with lower and higher proportions of ‘absorbing’ and ‘non-absorbing’ peptides, respectively. The higher yield of ‘non-absorbing’ peptides for infant digestion may permit strategic release of peptides with receptor-antagonistic bioactivity along the gut, and/or may promote supply of nitrogen for the microbiota. The favouring of digestion-resistant peptides to the colon due to processing requires further research to also investigate potential negative relationships with health.

BRAF protein immunoprecipitation, elution, and digestion from cell extract using a microfluidic mixer for mutant BRAF protein quantification by mass spectrometry.

This study utilized a microfluidic mixer for the sample pretreatment of cell extracts for target protein quantification by mass spectrometers, including protein immunoprecipitation and protein enzymatic digestion. The time of sample pretreatment was reduced and thus the throughput of quantitative mutant proteins was increased by using the proposed method. Whole cell lysates of the cancer cell line HT-29 with gene mutations were used as the sample. The target protein BRAF was immunoprecipitated using magnetic beads in a pneumatic micromixer. Purified protein was then eluted and digested by trypsin in another two micromixers to yield peptide fragments in the solution. Using stable isotope-labeled standard as the internal control, wild-type and mutant BRAF proteins were quantified using mass spectrometry, which could be used for cancer screening. Compared with conventional methods in which protein immunoprecipitation lasts overnight, the micromixer procedure takes only 1h, likely improving the throughput of mutant BRAF protein quantification by mass spectrometry. Graphical abstract Three micromixers were used to reduce the sample pretreatment time of cell extracts for target protein quantification by mass spectrometers, including protein immunoprecipitation, protein elution, and protein enzymatic digestion.

Nuts and Bolts of Protein Quantification by Online Trypsin Digestion Coupled LC-MS/MS Analysis.

Protein digestion coupled to liquid chromatography and tandem mass spectrometry (LC-MS/MS) detection enables multiplexed quantification of proteins in complex biological matrices. However, the reproducibility of enzymatic digestion of proteins to produce proteotypic target peptides is a major limiting factor of assay precision. Online digestion using immobilized trypsin addresses this problem through precise control of digestion conditions and time. Because online digestion is typically for a short time, the potential for peptide degradation, a major source of measurement bias, is significantly reduced. Online proteolysis requires minimal sample preparation and is easily coupled to LC-MS/MS systems, further reducing potential method variability. We describe herein a method optimized for the multiplexed quantification of several apolipoproteins in human serum using on-column digestion. We highlight key features of the method that enhance assay accuracy and precision. These include the use of value-assigned serum as calibrators and stable isotope-labeled (SIL) peptide analogs as internal standards. We also comment on practical aspects of column switching valve design, instrument maintenance, tandem mass spectrometry data acquisition, and data processing.

A4646 A novel endothelial NO-dependent vasorelaxing and anti-hypertensive peptide derived from rice bran

Objectives: We recently identified a novel anti-hypertensive peptide Leu-Arg-Ala (LRA) from the enzymatic digestion of rice bran protein (Shobako et al., Mol. Nutr. Food res., 2018). Orally administered LRA at a dose of 0.25 mg/kg potently reduced the systolic blood pressure (SBP) in spontaneously hypertensive rats (SHRs), but had low ACE inhibitory activity (IC50 = 62 μM), explaining its potent hypotensive activity. In this study, we investigated vasorelaxing activity of LRA and the involvement of nitric oxide (NO) signaling. Methods: The vasorelaxing activity was determined by the mesenteric artery isolated from SHRs. Changes in SBP of SHRs were measured by tail-cuff method. Results: A novel rice bran-derived hypotensive peptide LRA exhibited vasorelaxing activity in the mesenteric artery of SHRs. Pretreatment with NG-Nitro-L-arginine methyl ester (L-NAME), an inhibitor of NO synthase (NOS), diminished the LRA-induced vasorelaxing activity. L-NAME also inhibited the anti-hypertensive effects of LRA. LRA also activated phosphorylation of endothelial NOS in human umbilical vein endothelial cells (HUVECs). Thus, these data suggest that LRA-induced vasorelaxing and anti-hypertensive activites were mediated by the activation of endothelial NO signaling. Next, we investigated mechanisms upstream of NO signaling. The LRA-induced vasorelaxant activity was not blocked by HOE 140 (bradykinin B2 antagonist), A779 (MAS antagonist) and wortomannin (PI3 kinase inhibitor), implying that NO-mediated vasorelaxing activity by LRA is independent of the bradykinin B2/MAS receptor-PI3 kinase activation. Conclusion: We found that LRA possibly exhibited vasorelaxing and hypotensive effects in a novel endothelial NO signaling-dependent manner. This is the first example of a NO-dependent vasorelaxing peptide identified from rice bran.

Esophageal groove dysfunction: a cause of ruminal bloat in newborn calves

BackgroundEsophageal groove dysfunction is one of the major causes of ruminal bloat. This condition is fatal in new born calves if it is not treated early. In healthy, suckling calves, milk should bypass the forestomach (rumen and reticulum) and enter into the abomasum where enzymatic digestion of milk proteins takes place. However, failure of the esophageal groove allows milk to enter into the forestomach, which results in the production of excess gases by microbial fermentation. Consequently, this increase in abdominal distention particularly on the left side in ruminants is an imminent manifestation of excess gases in the foresomach.Case presentationA 10-day-old crossbred male calf presented with a distended left abdomen and manifesting dyspnea at a dairy farm. The calf was weak, reluctant to move, and had visibly congested mucus membranes. Regarding the calf’s feeding, milk was the only thing ingested and the calf had not started on dry feeds (hay, concentrates, and roughages). According to the herdsman of the farm, the calf had a mild-to-moderate form of bloat and 3–5 h after milk feeding the bloat would disappear spontaneously. During bloat, an increase in pulse rate, respiratory rate (tachypnea), and shallow breathing was noted. Physical examination revealed severe distention of the left side of the abdomen, and on percussion, accumulation of gases mixed with fluid in the left abdomen was detected. An attempt was made to release gases from forestomach by introducing a stomach tube with oral antibiotics; however, the case was not resolved. The calf suffered from frequent recurrence of bloat after every milk feed, and in response to the refractory outcome to conventional treatment, a rumenostomy was indicated and a better treatment response was achieved. In addition, IV fluid and other supportive therapy were provided while milk was withheld. However, considering the fact that milk is a natural feed that should not be taken away from every calf at this age, we had to encourage calf to consume milk as it would not result in bloat as far as rumen fistula is being created. Furthermore, encouraging calves to consume starter feed (fresh grasses and hay) earlier than usual recommended period whilst decreasing milk intake would hasten the rumen function.ConclusionsCases like this are successfully managed by a rumenostomy when conventional options fail.

Effect of Supplementation of a Whey Peptide Rich in Tryptophan-Tyrosine-Related Peptides on Cognitive Performance in Healthy Adults: A Randomized, Double-Blind, Placebo-Controlled Study.

Background: Previous epidemiological and clinical studies have shown that dairy products have beneficial effects on cognitive decline and dementia. Enzymatic digestion of whey protein produces a whey peptide rich in tryptophan-tyrosine-related peptides which improve cognitive performance in mice. We evaluated the effects of whey peptides on cognitive functions in healthy adults in a randomized, double-blind, placebo-controlled design. Methods: 101 healthy adults (45 to 64 years), with a self-awareness of cognitive decline received either whey peptide or placebo supplements for 12 weeks. Changes in cognitive function were assessed using neuropsychological tests at 6 and 12 weeks after the start of supplementation. Results: Verbal fluency test (VFT) score changes tended to be higher in the whey peptide group compared with the placebo at 12 weeks. Subgroup analysis classified by the degree of subjective fatigue showed that changes in the VFT as well as the Stroop and subjective memory function tests between baseline and 6 weeks of intervention were significantly better in subjects with high-level fatigue from the whey peptide group as compared to the placebo group. Conclusions: Intake of whey peptide might improve cognitive function in healthy middle- and older-aged adults with high subjective fatigue levels. Further studies will elucidate the relationship among cognitive improvement, whey peptides, and psychological fatigue.