Trypsin immobilization on three monolithic disks for on-line protein digestion

Easy, Robust, and Repeatable Online Acid Cleavage of Proteins in Mobile Phase for Fast Quantitative LC-MS Bottom-Up Protein Analysis─Application for Ricin Detection

Sample preparation involving the cleavage of proteins into peptides is the first critical step for successful bottom-up proteomics and protein analyses. Time- and labor-intensiveness are among the bottlenecks of the commonly used methods for protein sample preparation. Here, we report a fast online method for postinjection acid cleavage of proteins directly in the mobile phase typically used for LC-MS analyses in proteomics. The chemical cleavage is achieved in 0.1% formic acid within 35 s in a capillary heated to 195 °C installed upstream of the analytical column, enabling the generated peptides to be separated. The peptides generated by the optimized method covered the entire sequence except for one amino acid of trastuzumab used for the method development. The qualitative results are extraordinarily stable, even over a long period of time. Moreover, the method is also suitable for accurate and repeatable quantification. The procedure requires only one manual step, significantly decreasing sample transfer losses. To demonstrate its practical utility, we tested the method for the fast detection of ricin. Ricin can be unambiguously identified from an injection of 10 ng, and the results can be obtained within 7-8 min after receiving a suspicious sample. Because no sophisticated accessories and no additional reagents are needed, the method can be seamlessly transferred to any laboratory for high-throughput proteomic workflows.

Singlet oxygen generation for selective oxidation of emerging pollutants in a flow-by electrochemical system based on natural air diffusion cathode

The decay of free radicals involved in side reactions is one of the challenges faced by electrochemical degradation of organic pollutants. To this end, a non-radical oxidation system was constructed by a natural air diffusion cathode (ADC) and a Ti-based dimensional stable anode coated by RuO₂ (RuO₂-Ti anode) for cathodic hydrogen peroxide activation by anodic chlorine evolution. The ADC fabricated by the carbon black of BP2000 produced a stable concentration of hydrogen peroxide of 339.94 mg L^-1 (current efficiency of 73.4%) without aeration, which was superior to the cathode made by the XC72 carbon black. The flow-by ADC-RuO₂ system consisted of an ADC and a RuO₂-Ti anode showed high selectivity to aniline (AN) compared to benzoate (BA) in a NaCl electrolyte, whose degradation efficiencies were 97.72% and 1.3%, respectively. Rapid degradations of a mixture of emerging pollutants and AN were also observed in the ADC-RuO₂ system, with pseudo-first-order kinetic constants of 0.51, 1.29, 0.89, and 0.99 min^-1 for Bisphenol A (BPA), tetracycline (TC), sulfamethoxazole (SMX) and AN, respectively. Quenching experiments revealed the main reactive oxygen species for the pollutant degradation was singlet oxygen (¹O₂), which was also identified by the electron spin resonance (ESR) analysis. Finally, the steady-stable content of ¹O₂ was quantitatively determined to be 6.25 × 10^-11 M by the method of furfuryl alcohol (FFA) probe. Our findings provide a fast, low energy consumption and well controlled electrochemical oxidation method for selective degradation of organic pollutants. H₂O₂ generated on an air diffusion cathode by naturally diffused O₂, reacts with ClO^- produced from chloride oxidation on the RuO₂-Ti anode to form singlet oxygen (¹O₂). The electrochemical system shows an efficient oxidation to electron-rich emerging pollutants including bisphenol A, tetracycline, sulfamethoxazole and aniline, but a poor performance on the electron-deficient compounds (e.g., benzoate).

Potential and Scale-Up of Pore-Through-Flow Membrane Reactors for the Production of Prebiotic Galacto-Oligosaccharides with Immobilized β-Galactosidase

The production of prebiotics like galacto-oligosaccharides (GOS) on industrial scale is becoming more important due to increased demand. GOS are synthesized in batch reactors from bovine lactose using the cost intensive enzyme β-galactosidase (β-gal). Thus, the development of sustainable and more efficient production strategies, like enzyme immobilization in membrane reactors are a promising option. Activated methacrylatic monoliths were characterized as support for covalent immobilized β-gal to produce GOS. The macroporous monoliths act as immobilized pore-through-flow membrane reactors (PTFR) and reduce the influence of mass-transfer limitations by a dominating convective pore flow. Monolithic designs in the form of disks (0.34 mL) and for scale-up cylindric columns (1, 8 and 80 mL) in three different reactor operation configurations (semi-continuous, continuous and continuous with recirculation) were studied experimentally and compared to the free enzyme system. Kinetic data, immobilization efficiency, space-time-yield and long-term stability were determined for the immobilized enzyme. Furthermore, simulation studies were conducted to identify optimal operation conditions for further scale-up. Thus, the GOS yield could be increased by up to 60% in the immobilized PTFRs in semi-continuous operation compared to the free enzyme system. The enzyme activity and long-time stability was studied for more than nine months of intensive use.

Development of an In-Line Enzyme Reactor Integrated into a Capillary Electrophoresis System

The goal of this paper was to develop an in-line immobilized enzyme reactor (IMER) integrated into a capillary electrophoresis platform. In our research, we created the IMER by adsorbing trypsin onto the inner surface of a capillary in a short section. Enzyme immobilization was possible due to the electrostatic attraction between the oppositely charged fused silica capillary surface and trypsin. The reactor was formed by simply injecting and removing trypsin solution from the capillary inlet (~1–2 cms). We investigated the factors affecting the efficiency of the reactor. The main advantages of the proposed method are the fast, cheap, and easy formation of an IMER with in-line protein digestion capability. Human tear samples were used to test the efficiency of the digestion in the microreactor.

Study of the geometry of open channels in a layer-bed-type microfluidic immobilized enzyme reactor

This paper aims at studying open channel geometries in a layer-bed-type immobilized enzyme reactor with computer-aided simulations. The main properties of these reactors are their simple channel pattern, simple immobilization procedure, regenerability, and disposability; all these features make these devices one of the simplest yet efficient enzymatic microreactors. The high surface-to-volume ratio of the reactor was achieved using narrow (25–75 μm wide) channels. The simulation demonstrated that curves support the mixing of solutions in the channel even in strong laminar flow conditions; thus, it is worth including several curves in the channel system. In the three different designs of microreactor proposed, the lengths of the channels were identical, but in two reactors, the liquid flow was split to 8 or 32 parallel streams at the inlet of the reactor. Despite their overall higher volumetric flow rate, the split-flow structures are advantageous due to the increased contact time. Saliva samples were used to test the efficiencies of the digestions in the microreactors.

Flow-through enzymatic reactors using polymer monoliths: From motivation to application

The application of monolithic materials as carriers for enzymes has rapidly expanded to the realization of flow-through analysis and bioconversion processes. This expansion is partly attributed to the absence from diffusion limitation in many monoliths-based enzyme reactors. Particularly, the relatively ease of introducing functional groups renders polymer monoliths attractive as enzyme carriers. After summarizing the motivation to develop enzymatic reactors using polymer monoliths, this review reports the most recent applications of such reactors. Besides, the present review focuses on the crucial characteristics of polymer monoliths affecting the immobilization of enzymes and the processing parameters dictating the performance of the resulting enzymatic reactors. This review is intended to provide a guideline for designing and applying flow-through enzymatic reactors using polymer monoliths.

Fabrication of immobilized enzyme reactors with pillar arrays into polydimethylsiloxane microchip

This paper demonstrates the design, efficiency and applicability of a simple and inexpensive microfluidic immobilized enzymatic reactor (IMER) for rapid protein digestion. The high surface-to-volume ratio (S/V) of the reactor was achieved by forming pillars in the channel. It was found that pillar arrays including dimensions of 40 μm × 40 μm as pillar diameter and interpillar distance can provide both relatively high S/V and flow rate in the PDMS chip, the fabrication of which was performed by means of soft lithography using average research laboratory infrastructure. CZE peptide maps of IMER-based digestions were compared to peptide maps obtained from standard in-solution digestion of proteins. The peak patterns of the electropherograms and the identified proteins were similar, however, digestion with the IMER requires less than 10 min, while in-solution digestion takes 16 h.

A flow-through nanoporous alumina trypsin bioreactor for mass spectrometry peptide fingerprinting

Mass spectrometry-based proteomics benefits from efficient digestion of protein samples. In this study, trypsin was immobilized on nanoporous anodized alumina membranes to create an enzyme reactor suitable for peptide mass fingerprinting. The membranes were derivatized with 3-aminopropyltriethoxysilane and the amino groups were activated with carbonyldiimidazole to allow coupling of porcine trypsin via ε-amino groups. The function was assessed using the artificial substrate Nα-Benzoyl-L-arginine 4-nitroanilide hydrochloride, bovine ribonuclease A and a human plasma sample. A 10-membrane flow-through reactor was used for fragmentation and MS analysis after a single pass of substrate both by collection of product and subsequent off-line analysis, and by coupling on-line to the instrument. The peptide pattern allowed correct identification of the single target protein in both cases, and of >70 plasma proteins in single pass mode followed by LC-MS analysis. The reactor retained 76% of the initial activity after 14days of storage and repeated use at room temperature.

SIGNIFICANCE

This manuscript describes the design of a stable enzyme reactor that allows efficient and fast digestion with negligible leakage of enzyme and enzyme fragments. The high stability facilitates the use in an online-setup with MS detection since it allows the processing of multiple samples within an extended period of time without replacement.

Multichannel Open Tubular Enzyme Reactor Online Coupled with Mass Spectrometry for Detecting Ricin

For counterterrorism purposes, a selective nano liquid chromatography-mass spectrometry (nanoLC-MS) platform was developed for detecting the highly lethal protein ricin from castor bean extract. Manual sample preparation steps were omitted by implementing a trypsin/Lys-C enzyme-immobilized multichannel reactor (MCR) consisting of 126 channels (8 μm inner diameter in all channels) that performed online digestion of proteins (5 min reaction time, instead of 4-16 h in previous in-solution methods). Reduction and alkylation steps were not required. The MCR allowed identification of ricin by signature peptides in all targeted mode injections performed, with a complete absence of carry-over in blank injections. The MCRs (interior volume ≈ 1 μL) have very low backpressure, allowing for trivial online coupling with commercial nanoLC-MS systems. The open tubular nature of the MCRs allowed for repeatable within/between-reactor preparation and performance.

Performance comparison of three trypsin columns used in liquid chromatography

Trypsin is the most widely used enzyme in proteomic research due to its high specificity. Although the in-solution digestion is predominantly used, it has several drawbacks, such as long digestion times, autolysis, and intolerance to high temperatures or organic solvents. To overcome these shortcomings trypsin was covalently immobilized on solid support and tested for its proteolytic activity. Trypsin was immobilized on bridge-ethyl hybrid silica sorbent with 300Å pores, packed in 2.1×30mm column and compared with Perfinity and Poroszyme trypsin columns. Catalytic efficiency of enzymatic reactors was tested using N_α-Benzoyl-l-arginine 4-nitroanilide hydrochloride as a substrate. The impact of buffer pH, mobile phase flow rate, and temperature on enzymatic activity was investigated. Digestion speed generally increased with the temperature from 20 to 37°C. Digestion speed also increased with pH from 7.0 to 9.0; the activity of prototype enzyme reactor was highest at pH 9.0, when it activity exceeded both commercial reactors. Preliminary data for fast protein digestion are presented.

Optimization of Penicillium aurantiogriseum protease immobilization on magnetic nanoparticles for antioxidant peptides' obtainment

This work reports an optimization of protease from Penicillium aurantiogriseum immobilization on polyaniline-coated magnetic nanoparticles for antioxidant peptides' obtainment derived from bovine casein. Immobilization process was optimized using a full two-level factorial design (2⁴) followed by a response surface methodology. Using the derivative, casein was hydrolyzed uncovering its peptides that were sequenced and had antioxidant properties tested through (2,2'-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt) (ABTS) radical scavenging and hydrogen peroxide scavenging assays. Optimal conditions for immobilization were 2 hr of immobilization, offered protein amount of 200 µg/mL, immobilization pH of 6.3 and 7.3 hr of activation. Derivative keeps over 74% of its original activity after reused five times. Free and immobilized enzyme casein hydrolysates presented similar peptide mass fingerprints, and prevalent peptides could be sequenced. Hydrolysates presented more than 2.5× higher ROS scavenging activity than nonhydrolyzed casein, which validates the immobilized protease capacity to develop casein-derived natural ingredients with potential for functional foods.

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.

High efficiency and quantitatively reproducible protein digestion by trypsin-immobilized magnetic microspheres

Aldehyde- and NHS-activated magnetic microspheres were used to immobilize trypsin (CHO-trypsin and NHS-trypsin), and their performance for protein digestion was evaluated by reversed phase liquid chromatography-electrospray ionization-tandem mass spectrometry using an LTQ Orbitrap Velos instrument. NHS-trypsin provided greater sequence coverage and identified more peptides for the digestion of bovine serum albumin. A 1-min digestion at room temperature using the immobilized trypsin also identified more peptides (96±6 vs. 48±1) and produced higher sequence coverage (90±2% vs. 75±2%) than traditional free trypsin digestion for 12h at 37 °C. Analysis of 15 nM (0.001 mg/mL) BSA digested by NHS-trypsin in 1 min at room temperature consistently yielded one detected peptide; 150 nM BSA generated 22 peptides. Peptide intensity and protein spectral count were used to evaluate the run-to-run digestion reproducibility of NHS-trypsin with a three-protein-mixture. Three high intensity peptides for each protein generated intensity ratios from 0.70 to 1.09 and spectral count ratios from 0.78 to 1.18. Finally, RAW 264.7 cell lysates were digested by NHS-trypsin for 10 min and 30 min at room temperature, 604 and 697 protein groups, respectively, were identified by RPLC-ESI-MS/MS, with a peptide false discovery rate of less than 1%. Digestion by solution phase trypsin for 12h at 37 °C resulted in identification of 878 protein groups.

Studying protein-protein affinity and immobilized ligand-protein affinity interactions using MS-based methods

This review discusses the most important current methods employing mass spectrometry (MS) analysis for the study of protein affinity interactions. The methods are discussed in depth with particular reference to MS-based approaches for analyzing protein-protein and protein-immobilized ligand interactions, analyzed either directly or indirectly. First, we introduce MS methods for the study of intact protein complexes in the gas phase. Next, pull-down methods for affinity-based analysis of protein-protein and protein-immobilized ligand interactions are discussed. Presently, this field of research is often called interactomics or interaction proteomics. A slightly different approach that will be discussed, chemical proteomics, allows one to analyze selectivity profiles of ligands for multiple drug targets and off-targets. Additionally, of particular interest is the use of surface plasmon resonance technologies coupled with MS for the study of protein interactions. The review addresses the principle of each of the methods with a focus on recent developments and the applicability to lead compound generation in drug discovery as well as the elucidation of protein interactions involved in cellular processes. The review focuses on the analysis of bioaffinity interactions of proteins with other proteins and with ligands, where the proteins are considered as the bioactives analyzed by MS.

Liquid-chromatographic and mass-spectrometric identification of lens proteins using microwave-assisted digestion with trypsin-immobilized magnetic nanoparticles

We used a newly developed method combining trypsin-immobilized magnetic nanoparticles (TIMNs) and microwave-assisted protein digestion to study the proteins of human lens tissue. The digested proteins were identified by liquid chromatography and mass spectrometry. The lens proteins were digested under optimized conditions (digestion time 1 min, microwave power 400 W, trypsin-to-protein ratio 1:5) determined using bovine serum albumin as the standard protein, before liquid-chromatographic and mass-spectrometric analysis. Twenty-six proteins were identified with the new digestion method compared with 11 proteins identified with traditional in-solution digestion (12h). gamma-Crystallin, beta-crystallin, and superoxide dismutase 1 proteins, identified with the microwave-assisted method but not the traditional method, are related to cataract development according to some studies. The TIMNs were easily separated from the digestion products. This new digestion method could prove extremely useful for large-scale proteomic analyses.