Rapid Protein Digestion Research Articles

Low back-pressure hierarchically structured multichannel microfluidic bioreactors for rapid protein digestion – Proof of concept

A novel, easy-to-fabricate monolithic enzymatic microreactor with a hierarchical, torturous structure of flow-through channels of micrometric sizes and large mesopores was shown to enable rapid and very efficient digestion of proteins at high yields and exceptionally low back-pressures. Four silica monoliths with bi-modal 3D pore structure in micrometer and nanometer size scales were synthesized and characterized for structural and flow properties. The monolith with the highest total pore volume (4cm3/g) and flow-through channels 20–30μm in size, was further functionalized with trypsin to obtain multichannel immobilized enzyme (proteolytic) reactor (IMER). The value of permeability coefficient K evaluated for water (∼2.0·10−11) was found to be two orders of magnitude higher in the novel reactor than reported before for high-performance IMERs, enabling the flow rates of 750mL/cm2min at pressure gradients of 64kPa/cm. Very high practical potentials of the novel microbioreactor were demonstrated in the proteolysis of cytochrome c (Cyt-c) and myoglobin (Myo), without any earlier pretreatment. MALDI-TOF/TOF mass spectrometry analysis of sequence coverage was high: 70% (Cyt-c) and 90% (Myo) for 24min digestion, and 39% (Cyt-c) and 53% (Myo) when the proteolysis time was reduced to 2.4min. The proposed microreactors make full use of all advantages of microfuidic devices and mesoporous biocatalysts, and offer exceptional possibilities for biochemical/proteolytic applications in both large (production) and small (analytical) scales.

C-STrap Sample Preparation Method—In-Situ Cysteinyl Peptide Capture for Bottom-Up Proteomics Analysis in the STrap Format

Recently we introduced the concept of Suspension Trapping (STrap) for bottom-up proteomics sample processing that is based upon SDS-mediated protein extraction, swift detergent removal and rapid reactor-type protein digestion in a quartz depth filter trap. As the depth filter surface is made of silica, it is readily modifiable with various functional groups using the silane coupling chemistries. Thus, during the digest, peptides possessing specific features could be targeted for enrichment by the functionalized depth filter material while non-targeted peptides could be collected as an unbound distinct fraction after the digest. In the example presented here the quartz depth filter surface is functionalized with the pyridyldithiol group therefore enabling reversible in-situ capture of the cysteine-containing peptides generated during the STrap-based digest. The described C-STrap method retains all advantages of the original STrap methodology and provides robust foundation for the conception of the targeted in-situ peptide fractionation in the STrap format for bottom-up proteomics. The presented data support the method’s use in qualitative and semi-quantitative proteomics experiments.

Jejunal Casein Feeding Is Followed by More Rapid Protein Digestion and Amino Acid Absorption When Compared with Gastric Feeding in Healthy Young Men ,

Background: Dietary protein is required to attenuate the loss of muscle mass and to support recovery during a period of hospitalization. Jejunal feeding is preferred over gastric feeding in patients who are intolerant of gastric feeding. However, the impact of gastric vs. jejunal feeding on postprandial dietary protein digestion and absorption kinetics in vivo in humans remains largely unexplored.Objective: We compared the impact of gastric vs. jejunal feeding on subsequent dietary protein digestion and amino acid (AA) absorption in vivo in healthy young men.Methods: In a randomized crossover study design, 11 healthy young men (aged 21 ± 2 y) were administered 25 g specifically produced intrinsically L-[1-13C]phenylalanine–labeled intact casein via a nasogastric and a nasojejunal tube placed ~30 cm distal to the ligament of Treitz. Protein was provided in a 240-mL solution administered over a 65-min period in both feeding regimens. Blood samples were collected during the 7-h postprandial period to assess the increase in plasma AA concentrations and dietary protein–derived plasma L-[1-13C]phenylalanine enrichment.Results: Jejunal feeding compared with gastric feeding resulted in higher peak plasma phenylalanine, leucine, total essential AA (EAA), and total AA concentrations (all P < 0.05). This was attributed to a more rapid release of dietary protein–derived AAs into the circulation, as evidenced by a higher peak plasma L-[1-13C]phenylalanine enrichment concentration (2.9 ± 0.2 vs. 2.2 ± 0.2 mole percent excess; P < 0.05). The total postprandial plasma AA incremental area under the curve and time to peak did not differ after jejunal vs. gastric feeding. Plasma insulin concentrations increased to a greater extent after jejunal feeding when compared with gastric feeding (275 ± 38 vs. 178 ± 38 pmol/L; P < 0.05).Conclusions: Jejunal feeding of intact casein is followed by more rapid protein digestion and AA absorption when compared with gastric feeding in healthy young men. The greater postprandial increase in circulating EAA concentrations may allow a more robust increase in muscle protein synthesis rate after jejunal vs. gastric casein feeding. This trial was registered at trialregister.nl as NTR2801.

Rapid Online Non-Enzymatic Protein Digestion Analysis with High Pressure Superheated ESI-MS.

Recently, we reported a new ESI ion source that could electrospray the super-heated aqueous solution with liquid temperature much higher than the normal boiling point (J. Am. Soc. Mass Spectrom. 25, 1862-1869). The boiling of liquid was prevented by pressurizing the ion source to a pressure greater than atmospheric pressure. The maximum operating pressure in our previous prototype was 11 atm, and the highest achievable temperature was 180°C. In this paper, a more compact prototype that can operate up to 27 atm and 250°C liquid temperatures is constructed, and reproducible MS acquisition can be extended to electrospray temperatures that have never before been tested. Here, we apply this super-heated ESI source to the rapid online protein digestion MS. The sample solution is rapidly heated when flowing through a heated ESI capillary, and the digestion products are ionized by ESI in situ when the solution emerges from the tip of the heated capillary. With weak acid such as formic acid as solution, the thermally accelerated digestion (acid hydrolysis) has the selective cleavage at the aspartate (Asp, D) residue sites. The residence time of liquid within the active heating region is about 20 s. The online operation eliminates the need to transfer the sample from the digestion reactor, and the output of the digestive reaction can be monitored and manipulated by the solution flow rate and heater temperature in a near real-time basis.

Nanostructured microfluidic digestion system for rapid high-performance proteolysis.

A novel microfluidic protein digestion system with a nanostructured and bioactive inner surface was constructed by an easy biomimetic self-assembly strategy for rapid and effective proteolysis in 2 minutes, which is faster than the conventional overnight digestion methods. It is expected that this work would contribute to rapid online digestion in future high-throughput proteomics.

Histology-directed microwave assisted enzymatic protein digestion for MALDI MS analysis of mammalian tissue.

This study presents on-tissue proteolytic digestion using a microwave irradiation and peptide extraction method for in situ analysis of proteins from spatially defined regions of a tissue section. The methodology utilizes hydrogel discs (1 mm diameter) embedded with trypsin solution. The enzyme-laced hydrogel discs are applied to a tissue section, directing enzymatic digestion to a spatially confined area of the tissue. By applying microwave radiation, protein digestion is performed in 2 min on-tissue, and the extracted peptides are then analyzed by matrix assisted laser desorption/ionization mass spectrometry (MALDI MS) and liquid chromatography tandem mass spectrometry (LC-MS/MS). The reliability and reproducibility of the microwave assisted hydrogel mediated on-tissue digestion is demonstrated by the comparison with other on-tissue digestion strategies, including comparisons with conventional heating and in-solution digestion. LC-MS/MS data were evaluated considering the number of identified proteins as well as the number of protein groups and distinct peptides. The results of this study demonstrate that rapid and reliable protein digestion can be performed on a single thin tissue section while preserving the relationship between the molecular information obtained and the tissue architecture, and the resulting peptides can be extracted in sufficient abundance to permit analysis using LC-MS/MS. This approach will be most useful for samples that have limited availability but are needed for multiple analyses, especially for the correlation of proteomics data with histology and immunohistochemistry.

Construction of a high-performance magnetic enzyme nanosystem for rapid tryptic digestion.

A magnetic enzyme nanosystem have been designed and constructed by a polydopamine (PDA)-modification strategy. The magnetic enzyme nanosystem has well defined core-shell structure and a relatively high saturation magnetization (Ms) value of 48.3 emu g−1. The magnetic enzyme system can realize rapid, efficient and reusable tryptic digestion of proteins by taking advantage of its magnetic core and biofunctional shell. Various standard proteins (e.g. cytochrome C (Cyt-C), myoglobin (MYO) and bovine serum albumin (BSA)) have been used to evaluate the effectiveness of the magnetic enzyme nanosystem. The results show that the magnetic enzyme nanosystem can digest the proteins in 30 minutes, and the results are comparable to conventional 12 hours in-solution digestion. Furthermore, the magnetic enzyme nanosystem is also effective in the digestion of low-concentration proteins, even at as low as 5 ng μL−1 substrate concentration. Importantly, the system can be reused several times, and has excellent stability for storage. Therefore, this work will be highly beneficial for the rapid digestion and identification of proteins in future proteomics.

PP286-SUN: Jejunal Casein Feeding is Followed by More Rapid Protein Digestion and Amino Acid Absorption When Compared with Gastric Feeding in Vivo in Humans

PP286-SUN: Jejunal Casein Feeding is Followed by More Rapid Protein Digestion and Amino Acid Absorption When Compared with Gastric Feeding in Vivo in Humans

An ultra-fast and highly efficient multiple proteases digestion strategy using graphene-oxide-based immobilized protease reagents

Highly efficient and rapid proteolytic digestion of proteins into peptides is a crucial step in shotgun-based proteome-analysis strategy. Tandem digestion by two or more proteases is demonstrated to be helpful for increasing digestion efficiency and decreasing missed cleavages, which results in more peptides that are compatible with mass-spectrometry analysis. Compared to conventional solution digestion, immobilized protease digestion has the obvious advantages of short digestion time, no self-proteolysis, and reusability. We proposed a multiple-immobilized proteases-digestion strategy that combines the advantages of the two digestion strategies mentioned above. Graphene-oxide (GO)-based immobilized trypsin and endoproteinase Glu-C were prepared by covalently attaching them onto the GO surface. The prepared GO-trypsin and GO-Glu-C were successfully applied in standard protein digestion and multiple immobilized proteases digestion of total proteins of Thermoanaerobacter tengcongensis. Compared to 12-hour solution digestion using trypsin or Glu-C, 14% and 7% improvement were obtained, respectively, in the sequence coverage of BSA by one-minute digestion using GO-trypsin and GO-Glu-C. Multiple immobilized-proteases digestion of the total proteins of Thermoanaerobacter tengcongensis showed 24.3% and 48.7% enhancement in the numbers of identified proteins than was obtained using GO-trypsin or GO-Glu-C alone. The ultra-fast and highly efficient digestion can be contributed to the high loading capacity of protease on GO, which leads to fewer missed cleavages and more complete digestion. As a result, improved protein identification and sequence coverage can be expected.

Characterizing rapid, activity‐linked conformational transitions in proteins via sub‐second hydrogen deuterium exchange mass spectrometry

This review outlines the application of time-resolved electrospray ionization mass spectrometry (TRESI-MS) and hydrogen-deuterium exchange (HDX) to study rapid, activity-linked conformational transitions in proteins. The method is implemented on a microfluidic chip which incorporates all sample-handling steps required for a 'bottom-up' HDX workflow: a capillary mixer for sub-second HDX labeling, a static mixer for HDX quenching, a microreactor for rapid protein digestion, and on-chip electrospray. By combining short HDX labeling pulses with rapid digestion, this approach provides a detailed characterization of the structural transitions that occur during protein folding, ligand binding, post-translational modification and catalytic turnover in enzymes. This broad spectrum of applications in areas largely inaccessible to conventional techniques means that microfluidics-enabled TRESI-MS/HDX is a unique and powerful approach for investigating the dynamic basis of protein function.

Intensive Protein Digestion Using Cross‐Linked Trypsin Aggregates in Proteomics Analysis

AbstractIn this study, cross‐linked enzyme aggregates of tissue‐culture‐grade trypsin (CLEAs‐T) were prepared and introduced to the proteomics analysis instead of the expensive proteomics‐grade trypsin, which benefits from the protein purification during the preparation of the CLEAs. Bovine serum albumin, lysozyme, bovine hemoglobin, and α‐casein were used as model proteins, and three intensive strategies (high‐enzyme‐concentration, high‐temperature, and ultrasound‐assisted digestion) were applied to the rapid and efficient digestion of model proteins by CLEAs‐T. The peptide fragments were then identified by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry, which revealed the higher sequence coverage and sharply reduced digestion time of these strategies compared with the conventional in‐solution 12 h digestion method. Morphology studies demonstrated that the excellent performance of CLEAs‐T in proteomics analysis came from the “scaffoldlike” supermolecular structure, which provided a high resistance to the autolysis and denaturation of trypsin under high‐enzyme‐concentration, high‐temperature, and ultrasound‐assisted digestion.

Thermostable trypsin conjugates immobilized to biogenic magnetite show a high operational stability and remarkable reusability for protein digestion

In this work, magnetosomes produced by microorganisms were chosen as a suitable magnetic carrier for covalent immobilization of thermostable trypsin conjugates with an expected applicability for efficient and rapid digestion of proteins at elevated temperatures. First, a biogenic magnetite was isolated from Magnetospirillum gryphiswaldense and its free surface was coated with the natural polysaccharide chitosan containing free amino and hydroxy groups. Prior to covalent immobilization, bovine trypsin was modified by conjugating with α-, β- and γ-cyclodextrin. Modified trypsin was bound to the magnetic carriers via amino groups using 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide and N-hydroxysulfosuccinimide as coupling reagents. The magnetic biomaterial was characterized by magnetometric analysis and electron microscopy. With regard to their biochemical properties, the immobilized trypsin conjugates showed an increased resistance to elevated temperatures, eliminated autolysis, had an unchanged pH optimum and a significant storage stability and reusability. Considering these parameters, the presented enzymatic system exhibits properties that are superior to those of trypsin forms obtained by other frequently used approaches. The proteolytic performance was demonstrated during in-solution digestion of model proteins (horseradish peroxidase, bovine serum albumin and hen egg white lysozyme) followed by mass spectrometry. It is shown that both magnetic immobilization and chemical modification enhance the characteristics of trypsin making it a promising tool for protein digestion.

Efficient proteolysis strategies based on microchip bioreactors

In proteome research, proteolysis is an important procedure prior to the mass spectrometric identification of proteins. The typical time of conventional in-solution proteolysis is as long as several hours to half a day. To enhance proteolysis efficiency, a variety of microchip bioreactors have been developed for the rapid digestion and identification of proteins in the past decade. This review mainly focuses on the recent advances and the key strategies of microchip bioreactors in protein digestion. The subjects covered include microchip proteolysis systems, the immobilization of proteases in microchannels, the applications of microchip bioreactors in highly efficient proteolysis, and future prospects. It is expected that microchip bioreactors will become powerful tools in protein analysis and will find a wide range of applications in high-throughput protein identification.

Measuring Dynamics in Weakly Structured Regions of Proteins Using Microfluidics-Enabled Subsecond H/D Exchange Mass Spectrometry

This work introduces an integrated microfluidic device for measuring rapid H/D exchange (HDX) in proteins. By monitoring backbone amide HDX on the millisecond to low second time scale, we are able to characterize conformational dynamics in weakly structured regions, such as loops and molten globule-like domains that are inaccessible in conventional HDX experiments. The device accommodates the entire MS-based HDX workflow on a single chip with residence times sufficiently small (ca. 8 s) that back-exchange is negligible (≤5%), even without cooling. Components include an adjustable position capillary mixer providing a variable-time labeling pulse, a static mixer for HDX quenching, a proteolytic microreactor for rapid protein digestion, and on-chip electrospray ionization (ESI). In the present work, we characterize device performance using three model systems, each illustrating a different application of 'time-resolved' HDX. Ubiquitin is used to illustrate a crude, high throughput structural analysis based on a single subsecond HDX time-point. In experiments using cytochrome c, we distinguish dynamic behavior in loops, establishing a link between flexibility and interactions with the heme prosthetic group. Finally, we localize an unusually high 'burst-phase' of HDX in the large tetrameric enzyme DAHP synthase to a 'molten globule-like' region surrounding the active site.

대량 발굴 프로테옴 분석을 위한 어쿠스틱 기술 기반 고속 단백질 절편화

최근 질량분석기와 다차원 크로마토그래피 분석법과 대용량 데이터를 처리하는 생물정보학 프로그램 등과 같은 복합적인 기술요소들의 발전은 대량 프로테옴을 분석하는 것을 가능하게 했다. 하지만, 이런 대량의 프로테옴을 분석하는 것은 단백질 절편화 과정의 긴 소요 시간과 낮은 재현성으로 인하여 한계를 가진다. 이 연구에서는 어쿠스틱 기술을 이용해 빠르게 단백질을 분해하는 새로운 방법을 제시했다. 이 어쿠스틱 기술의 시간과 강도를 최적화하기 위해서 여러 가지 조건에서 BSA 단백질을 트립신으로 절편화한 후 액체 크로마토그래피와 질량분석기로 분석하였다. 16시간동안 인큐베이션하는 기존의 방법과 슈퍼 어쿠스틱 기술을 사용한 방법을 비교하였을 때 슈퍼 어쿠스틱 기술이 기존의 방법보다 더 높은 아미노산 동정율을 보였으며, 유방암 세포와 같은 단백질 복합체에 적용하였을 때 30분의 절편화 시간에서도 효율적인 결과를 확인할 수 있었다. 이 새로운 방법은 샘플 전처리 과정에서 많은 양의 단백질일지라도 더 좋은 효율성을 가지게 되고 또한, 소비되는 시간도 줄여주며 일정 시간내의 샘플 처리량도 증가하게 된다. Recent developments and improvements of multiple technological elements including mass spectrometry (MS) instrument, multi-dimensional chromatographic separation, and software tools processing MS data resulted in benefits of large scale proteomics analysis. However, its throughput is limited by the speed and reproducibility of the protein digestion process. In this study, we demonstrated a new method for rapid proteolytic digestion of proteins using acoustic technology. Tryptic digests of BSA prepared at various conditions by super acoustic for optimization time and intensity were analyzed by LC-MS/MS showed higher sequence coverage in compared with traditional 16 hrs digestion method. The method was applied successfully for complex proteins of a breast cancer cells at 30 min of digestion at intensity 2. This new application reduces time-consuming of sample preparation with better efficiency, even with large amount of proteins, and increases high-throughput process in sample preparation state.

Erratum: Rapid and efficient protein digestion using trypsin‐coated magnetic nanoparticles under pressure cycles

Figure 2B in this paper is corrected as follows: (…) (B) Enzyme stabilities of CA-TR/NP (empty circles), EC-TR/NP (filled circles), and free trypsin (empty triangles) under recycled uses and shaking at 200 rpm at room temperature. The activity was measured by the hydrolysis of BAPNA at each time point, and the relative activity was calculated from the ratio of residual activity at each time point to the initial activity of each sample.

Efficient proteolysis using a regenerable metal‐ion chelate immobilized enzyme reactor supported on organic–inorganic hybrid silica monolith

A metal-ion chelate immobilized enzyme reactor (IMER) supported on organic-inorganic hybrid silica monolith was developed for rapid digestion of proteins. The monolithic support was in situ prepared in a fused silica capillary via the polycondensation between tetraethoxysilane hydrolytic sol and iminodiacetic acid conjugated glycidoxypropyltrimethoxysilane. After activated by Cu(2+) , trypsin was immobilized onto the monolithic support via metal chelation. Proteolytic capability of such an IMER was evaluated by the digestion of myoglobin and BSA, and the digests were further analyzed by microflow reversed-phase liquid chromatography with ESI-MS/MS. Similar sequence coverages of myoglobin and BSA were obtained by IMER, in comparison to those obtained by in-solution digestion (91 versus 92% for 200 ng myoglobin, and 26 versus 26% for 200 ng BSA). However, the digestion time was shortened from 12 h to 50 s. When the enzymatic activity was decreased after seven runs, the IMER could be easily regenerated by removing Cu(2+) via EDTA followed by trypsin immobilization with fresh Cu(2+) introduced, yielding the equal sequence coverage (26% for 200 ng BSA). For ∼5 μg rat liver extract, even more proteins were identified with the immobilized trypsin digestion within 150 s in comparison to the in-solution digestion for 24 h (541 versus 483), demonstrating that the IMER could be a promising tool for efficient and high-throughput proteome profiling.

Rapid and efficient protein digestion using trypsin‐coated magnetic nanoparticles under pressure cycles

Trypsin-coated magnetic nanoparticles (EC-TR/NPs), prepared via a simple multilayer random crosslinking of the trypsin molecules onto magnetic nanoparticles, were highly stable and could be easily captured using a magnet after the digestion was complete. EC-TR/NPs showed a negligible loss of trypsin activity after multiple uses and continuous shaking, whereas the conventional immobilization of covalently attached trypsin on NPs resulted in a rapid inactivation under the same conditions due to the denaturation and autolysis of trypsin. A single model protein, a five-protein mixture, and a whole mouse brain proteome were digested at atmospheric pressure and 37°C for 12 h or in combination with pressure cycling technology at room temperature for 1 min. In all cases, EC-TR/NPs performed equally to or better than free trypsin in terms of both the identified peptide/protein number and the digestion reproducibility. In addition, the concomitant use of EC-TR/NPs and pressure cycling technology resulted in very rapid (∼1 min) and efficient digestions with more reproducible digestion results.

Vortex‐assisted tryptic digestion

The effect of vortex-induced vibration during tryptic digestion was investigated by applying different vibrational speeds (0, 600, 1200, or 2500 rpm) to digestion solutions for varying durations (10, 20, 30, 40, or 60 min) at two different incubation temperatures (25°C or 37°C). The most rapid digestion was observed with the highest vibrational speed and temperature. With the application of 2500 rpm at 37°C, the tryptic digestion of each of three standard proteins (cytochrome c, myoglobin, or bovine serum albumin) provided complete disappearance of the protein within 60 min, as determined by matrix-assisted laser desorption/ionization mass spectrometry. Compared to conventional overnight digestion, 60-min vortex-assisted tryptic digestion generated longer peptides, due primarily to the limited digestion time and provided better sequence coverages (89% vs. 78% for cytochrome c, 100% vs. 87% for myoglobin, and 38% vs. 26% for BSA). The longer peptides should be advantageous to analytical methods such as the middle-down approach that benefit from increased sequence coverage of proteins. Vortex-assisted tryptic digestion is expected to be a useful method for rapid tryptic digestion of proteins.

Efficient Tryptic Proteolysis Accelerated by Laser Radiation for Peptide Mapping in Proteome Analysis

Back to basics: Coupled with MALDI-TOF MS, laser-assisted proteolysis (see schematic illustration) enabled rapid protein digestion and peptide mapping without the need for enzyme immobilization to increase the efficiency of tryptic digestion. Protein solutions containing trypsin were digested in less than a minute upon irradiation at 808 nm with a laser.