In-line system containing porous polymer monoliths for protein digestion with immobilized pepsin, peptide preconcentration and nano-liquid chromatography separation coupled to electrospray ionization mass spectroscopy

A review on the immobilization of pepsin: A Lys-poor enzyme that is unstable at alkaline pH values

Pepsin is a protease used in many different applications, and in many instances, it is utilized in an immobilized form to prevent contamination of the reaction product. This enzyme has two peculiarities that make its immobilization complex. The first one is related to the poor presence of primary amino groups on its surface (just one Lys and the terminal amino group). The second one is its poor stability at alkaline pH values. Both features make the immobilization of this enzyme to be considered a complicated goal, as most of the immobilization protocols utilize primary amino groups for immobilization. This review presents some of the attempts to get immobilized pepsin biocatalyst and their applications. The high density of anionic groups (Asp and Glu) make the anion exchange of the enzyme simpler, but this makes many of the strategies utilized to immobilize the enzyme (e.g., amino-glutaraldehyde supports) more related to a mixed ion exchange/hydrophobic adsorption than to real covalent immobilization. Finally, we propose some possibilities that can permit not only the covalent immobilization of this enzyme, but also their stabilization via multipoint covalent attachment.

Facile DNA adsorption enabling ammonium-based hydrophilic affinity monolithic column for high-performance online selective microextraction of ochratoxin A

Herein, a facile protocol of simple DNA adsorption on UV-initiated polymerization supports was proposed for effectively fabricating aptamer-based affinity monolithic column. Hydrophilic cationic monolith with an excellent mechanical stability was achieved within 7 min and then massive aptamers were directly bound by DNA charge-dependent adsorption. Strong cationic quaternary ammonium-based monomer was employed to provide effective and stable positive charge surface for aptamer immobilization in a wide range of pH. An ultra-high aptamer coverage density of 6813 pmol/μL was achieved to gain a highly specific online recognition performance. Limitations such as low aptamer capacity, tedious modification and time-consuming reactions in the traditional biological or covalent modification strategies were avoided. By using ochratoxin A (OTA) as the given analyte, the selective recognition and high recoveries were successfully achieved, and little cross-reactivity towards OTB analogue was only 0.5% even if the content of OTB got up to 125 folds of OTA. Applied to sample analysis, the satisfactory discriminations of trace OTA were obtained at 93.9 ± 1.9% - 96.5 ± 1.7%（n = 3）in beer, wheat and chicken liver samples. It might light a cost-effective access to efficiently preparing high-performance affinity monoliths towards the selective in-tube microextraction of OTA.

Tunable Polymeric Scaffolds for Enzyme Immobilization

The number of methodologies for the immobilization of enzymes using polymeric supports is continuously growing due to the developments in the fields of biotechnology, polymer chemistry, and nanotechnology in the last years. Despite being excellent catalysts, enzymes are very sensitive molecules and can undergo denaturation beyond their natural environment. For overcoming this issue, polymer chemistry offers a wealth of opportunities for the successful combination of enzymes with versatile natural or synthetic polymers. The fabrication of functional, stable, and robust biocatalytic hybrid materials (nanoparticles, capsules, hydrogels, or films) has been proven advantageous for several applications such as biomedicine, organic synthesis, biosensing, and bioremediation. In this review, supported with recent examples of enzyme-protein hybrids, we provide an overview of the methods used to combine both macromolecules, as well as the future directions and the main challenges that are currently being tackled in this field.

Investigating Monoliths (Vinyl Azlactone-co-Ethylene Dimethacrylate) as a Support for Enzymes and Drugs, for Proteomics and Drug-Target Studies

Prior to mass spectrometry, on-line sample preparation can be beneficial to reduce manual steps, increase speed, and enable analysis of limited sample amounts. For example, bottom-up proteomics sample preparation and analysis can be accelerated by digesting proteins to peptides in an on-line enzyme reactor. We here focus on low-backpressure 100 μm inner diameter (ID) × 160 mm, 180 μm ID × 110 mm or 250 μm ID × 140 mm vinyl azlactone-co-ethylene dimethacrylate [poly(VDM-co-EDMA)] monoliths as supports for immobilizing of additional molecules (i.e., proteases or drugs), as the monolith was expected to have few unspecific interactions. For on-line protein digestion, monolith supports immobilized with trypsin enzyme were found to be suited, featuring the expected characteristics of the material, i.e., low backpressure and low carry-over. Serving as a functionalized sample loop, the monolith units were very simple to connect on-line with liquid chromatography. However, for on-line target deconvolution, the monolithic support immobilized with a Wnt pathway inhibitor was associated with numerous secondary interactions when exploring the possibility of selectively trapping target proteins by drug-target interactions. Our initial observations suggest that (poly(VDM-co-EDMA)) monoliths are promising for e.g., on-line bottom-up proteomics, but not a "fit-for-all" material. We also discuss issues related to the repeatability of monolith-preparations.

Analyte-substrate interactions at functionalized tip electrospray ionization mass spectrometry: Molecular mechanisms and applications

Conventional electrospray ionization mass spectrometry (ESI-MS) commonly uses capillary tip for sample introduction and ionization. In recent years, ESI-MS using noncapillary substrate tips has attracted growing interest as it allows separation and enrichment of analytes from complex samples due to analytes-substrate interactions. In this work, model mixtures and functionalized tips were employed to investigate the molecular mechanism of the analyte-substrate interactions. The mixtures were directly loaded on substrate tips, and then temporal responses of analytes were investigated by monitoring selected ion chromatogram (SIC) responses of each analyte. It is found that all analytes are sprayed out together when bulk solution loaded substrate surface and then sequential ionization of analytes were observed. Sequential ionization of analytes was affected by the analytes-substrate interactions which caused analytes of weaker-interaction to be faster moved and the analytes of stronger-interactions to be retained on the substrate. The main molecular mechanisms of analyte-substrate interactions were revealed to be hydrophobic interactions and electrostatic interactions. Furthermore, based on the mechanistic insights, functionalized tips were further applied for rapid extractive sampling of target analytes from complex samples with good analytical performances. Overall, this study on the mechanism and applications of analyte-substrate interactions is useful for understanding the fundamental principles and further developments of functionalized tip electrospray ionization (TESI).

Porous organic cage incorporated monoliths for solid-phase extraction coupled with liquid chromatography-mass spectrometry for identification of ecdysteroids from Chenopodium quinoa Willd

Here, a porous organic cage (POC)-incorporated polymeric monolith was fabricated in a syringe through the introduction of the POC into poly(ethylene glycol dimethacrylate) monolith in a one-step traditional free-radical polymerization proceess. The resulting monolithic phases were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), Fourier-transform infrared spectroscopy (FT-IR), powder X-ray diffraction (PXRD), nitrogen adsorption/desorption experiments and thermogravimetric analysis (TGA), which confirmed the successful incorporation of the POC in the monolithic matrix. The functionality of the POC-incorporated poly(EDMA) monolith facilitated for the solid phase extraction (SPE) of 20-hydroxecdysone (an ecdysteroid) from Chenopodium quinoa Willd. extract coupled with UPLC-QqQ-MS/MS, exhibiting satisfactory accuracy (93-106%), precision (< 6.5%) and reusability. In addition, UPLC-Q-Exactive-Orbitrap-MS/MS analysis of the quinoa sample after SPE by POC-incorporated monolith provided the identification of 20-hydroxecdysone and three other ecdysteroids. These results demonstrate the potential of POC-incorporated monoliths for the SPE of ecdysteroids from complex plant systems.

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.

Thiol-ene Monolithic Pepsin Microreactor with a 3D-Printed Interface for Efficient UPLC-MS Peptide Mapping Analyses

To improve the sample handling, and reduce cost and preparation time, of peptide mapping LC-MS workflows in protein analytical research, we here investigate the possibility of replacing conventional enzymatic digestion methods with a polymer microfluidic chip based enzyme reactor. Off-stoichiometric thiol-ene is utilized as both bulk material and as a monolithic stationary phase for immobilization of the proteolytic enzyme pepsin. The digestion efficiency of the, thiol-ene based, immobilized enzyme reactor (IMER) is compared to that of a conventional, agarose packed bed, pepsin IMER column commonly used in LC-MS based protein analyses. The chip IMER is found to rival the conventional column in terms of digestion efficiency at comparable residence time and, using a 3D-printed interface, be directly interfaceable with LC-MS.

Advances in organic polymer-based monolithic column technology for high-resolution liquid chromatography-mass spectrometry profiling of antibodies, intact proteins, oligonucleotides, and peptides

This review focuses on the preparation of organic polymer-based monolithic stationary phases and their application in the separation of biomolecules, including antibodies, intact proteins and protein isoforms, oligonucleotides, and protein digests. Column and material properties, and the optimization of the macropore structure towards kinetic performance are also discussed. State-of-the-art liquid chromatography-mass spectrometry biomolecule separations are reviewed and practical aspects such as ion-pairing agent selection and carryover are presented. Finally, advances in comprehensive two-dimensional LC separations using monolithic columns, in particular ion-exchange×reversed-phase and reversed-phase×reversed-phase LC separations conducted at high and low pH, are shown.

Monoliths in capillary electrochromatography and capillary liquid chromatography in conjunction with mass spectrometry

Here, we have reviewed separation studies utilizing monolithic capillary columns for separation of compounds preceding MS analysis. The review is divided in two parts according to the used separation method, namely CEC and capillary LC (cLC). Based on our overview, monolithic CEC-MS technique have been more focused on the syntheses of highly specialized and selective separation phase materials for fast and efficient separation of specific types of analytes. In contrast, monolithic cLC-MS is more widely used and is often employed, for instance, in the analysis of oligonucleotides, metabolites, and peptides and proteins in proteomic studies. While poly(styrene-divinylbenzene)-based and silica-based monolithic capillaries found their place in proteomic analyses, the other laboratory-synthesized monoliths still wait for their wider utilization in routine analyses. The development of new monolithic materials will most likely continue due to the demand of more efficient and rapid separation of increasingly complex samples.

Immobilized pepsin microreactor for rapid peptide mapping with nanoelectrospray ionization mass spectrometry

Most enzymatic microreactors for protein digestion are based on trypsin, but proteins with hydrophobic segments may be difficult to digest because of the paucity of Arg and Lys residues. Microreactors based on pepsin, which is less specific than trypsin, can overcome this challenge. Here, an integrated immobilized pepsin microreactor (IPMR)/nanoelectrospray emitter is examined for its potential for peptide mapping. For myoglobin, equivalent sequence coverage is obtained in a thousandth the time of solution digestion with better sequence coverage. While sequence coverage of cytochrome c is lesser than solution in this short duration, more highly-charged peptic peptides are produced and a number of peaks are unidentified at low-resolution, suggesting that high-resolution mass spectrometry is needed to take full advantage of integrated IPMR/nanoelectrospray devices.

Recent advances on multidimensional liquid chromatography-mass spectrometry for proteomics: from qualitative to quantitative analysis--a review

With the acceleration of proteome research, increasing attention has been paid to multidimensional liquid chromatography-mass spectrometry (MDLC-MS) due to its high peak capacity and separation efficiency. Recently, many efforts have been put to improve MDLC-based strategies including "top-down" and "bottom-up" to enable highly sensitive qualitative and quantitative analysis of proteins, as well as accelerate the whole analytical procedure. Integrated platforms with combination of sample pretreatment, multidimensional separations and identification were also developed to achieve high throughput and sensitive detection of proteomes, facilitating highly accurate and reproducible quantification. This review summarized the recent advances of such techniques and their applications in qualitative and quantitative analysis of proteomes.

Azlactone-Functionalized Polymers as Reactive Platforms for the Design of Advanced Materials: Progress in the Last Ten Years

Polymers functionalized with azlactone (or oxazolone) functionality have become increasingly useful for the rapid and modular design of functional materials. Because azlactones can react via ring-opening reactions with a variety of different nucleophilic species (e.g., primary amines, hydroxyl groups, and thiol functionality), azlactone-functionalized materials can serve as convenient 'reactive' platforms for the post-synthesis or post-fabrication introduction of a broad range of chemical functionality to soluble polymers, insoluble supports, and surfaces/interfaces. The last decade has seen an increase in both the number and the variety of reports that exploit the properties and the reactivities of azlactone-functionalized polymers. Here, we highlight recent work from several different laboratories, including our own, toward the design and characterization of azlactone-functionalized polymers, with a particular emphasis on: (i) new synthetic approaches for the preparation of well-defined azlactone-functionalized polymers using living/controlled methods of polymerization, (ii) the design and modular synthesis of side-chain functionalized polymers and block copolymers via post-polymerization modification of azlactone-functionalized polymers, (iii) the development of reactive polymeric supports useful in the contexts of separations and catalysis, and (iv) methods for the fabrication of reactive thin films and other approaches to the immobilization of azlactone functionality on surfaces and interfaces. Examples discussed herein reveal a growing awareness of azlactone functionality as a useful tool for polymer chemists, and highlight several ways that the unique reactivity of these materials can both complement and provide useful alternatives to other reactive polymers currently used to design functional materials.

Polymer monolith-integrated multilayer poly(dimethylsiloxane) microchip for online microextraction and capillary electrophoresis

We reported the in situ synthesis and use of porous polymer monolith (PPM) columns in an integrated multilayer PDMS/glass microchip for microvalve-assisted on-line microextraction and microchip electrophoresis for the first time. Under the control of PDMS microvalves, the grafting of the microchannel surface and in situ photopolymerization of poly(methacrylic acid-co-ethylene glycol dimethacrylate) monolith in a defined zone were successfully achieved. Different factors including the surface grafting, polymerization time, PDMS elastic properties (ratio of oligomer/curing reagent) and UV intensity that affect the monolith synthesis in the PDMS microchannel were investigated and optimized. Dopamine, a model analyte, has been online microextracted, eluted, electrophoresized and electrochemically detected in the microchip, with a mean concentration enrichment factor of 80 (n=3). The results demonstrated that the PPM could be synthesized successfully in the PDMS microchip with a homogeneous structure and excellent mechanical properties. Furthermore, owing to the intrinsic character using PDMS in large-scale integrated microsystems, the implantation of PPM pretreatment units in PDMS microchips would make it possible to deal with complicated analytical processes in a high-throughput way.

Highly efficient enzyme reactors containing trypsin and endoproteinase LysC immobilized on porous polymer monolith coupled to MS suitable for analysis of antibodies

Capillary enzymatic microreactors containing trypsin and endoproteinase LysC immobilized on a porous polymer monolith have been prepared and used for the characterization and identification of proteins such as cytochrome c, bovine serum albumin, and high-molecular weight human immunoglobulin G. The hydrophilicity of diol functionalities originating from the hydrolyzed poly(glycidyl methacrylate-co-ethylene dimethacrylate) monolith was not sufficient to avoid adsorption of hydrophobic albumin in a highly aqueous mobile phase. Therefore, this monolith was first hydrophilized via photografting of poly(ethylene glycol) methacrylate followed by photografting of a 4-vinyl-2,2-dimethylazlactone to provide the pore surface with reactive functionalities required for immobilization. This new approach reduced the undesired nonspecific adsorption of proteins and peptides and facilitated control of both the enzyme immobilization and protein digestion processes. The enzymatic reactors were coupled off-line with MALDI/TOF MS and/or on-line with ESI/TOF MS. Experimental conditions for digestion were optimized using cytochrome c and bovine serum albumin as model proteins. The optimized reactors were then integrated into a multidimensional system comprised of a monolithic capillary enzyme reactor, an in-line nanoLC separation of peptides using a poly(lauryl methacrylate-co-ethylene dimethacrylate) monolithic column, and ESI/TOF MS. With the use of this system, immunoglobulin G was digested at room temperature in 6 min to an extent similar to that achieved with soluble enzyme at 37 degrees C after 24 h.

Functionalization of fibers using azlactone-containing polymers: layer-by-layer fabrication of reactive thin films on the surfaces of hair and cellulose-based materials

We report an approach to the functionalization of fibers and fiber-based materials that is based on the deposition of reactive azlactone-functionalized polymers and the "reactive" layer-by-layer assembly of azlactone-containing thin films. We demonstrate (i) that the azlactone-functionalized polymer poly(2-vinyl-4,4-dimethylazlactone) (PVDMA) can be used to modify the surfaces of a model protein-based fiber (horsehair) and cellulose-based materials (e.g., cotton and paper), and (ii) that fibers functionalized in this manner can be used to support the fabrication of covalently cross-linked and reactive polymer multilayers assembled using PVDMA and poly(ethyleneimine) (PEI). The growth, chemical reactivity, and uniformity of films deposited on these substrates were characterized using fluorescence microscopy, confocal microscopy, and scanning electron microscopy (SEM). In addition to the direct functionalization of fibers, we demonstrate that the residual azlactone functionality in PVDMA-treated or film-coated fibers can be exploited to chemically modify the surface chemistry and physicochemical properties of fiber-based materials postfabrication using amine functionalized molecules. For example, we demonstrate that this approach permits control over the surface properties of paper (e.g., absorption of water) by simple postfabrication treatment of film-coated paper with the hydrophobic amine n-decylamine. The azlactone functionality present in these materials provides a platform for the modification of polymer-treated and film-coated fibers with a broad range of other chemical and biological species (e.g., enzymes, peptides, catalysts, etc.). The results of this investigation thus provide a basis for the functionalization of fibers and fiber-based materials (e.g., textile fabrics or nonwoven mats) of potential utility in a broad range of consumer, industrial, and biomedical contexts.

Porous polymer monolithic column with surface-bound gold nanoparticles for the capture and separation of cysteine-containing peptides

A new porous polymer monolithic capillary column modified with gold nanoparticles that enables the selective capture of cysteine-containing peptides has been developed to reduce the complexity of peptide mixtures generated in bottom-up proteomic analysis. The column is prepared from a poly(glycidyl methacrylate-co-ethylene dimethacrylate) monolith through reaction of some of its epoxide moieties with cysteamine to afford a monolith rich in surface thiol groups. In situ reduction of chloroauric acid within the column is then used to form gold nanoparticles attached to the surface of the pores of the monolith. This process preserves the excellent hydrodynamic properties of the monolithic column while providing a means to selectively retain cysteine-containing peptides from an analyte due to their high affinity for gold. Release of the retained peptides is subsequently achieved with an excess of 2-mercaptoethanol. The loading capacity determined for l-cysteine using frontal elution is 2.58 mumol/m. Since the gold-thiol link is less stable at elevated temperatures, the adsorption capacity is recovered by washing the column at 80 degrees C for 2 h. While regeneration is easy, the multiplicity of bonds between the monolithic support and the gold nanoparticles prevents their elution even under harsh conditions such as treatment with pure 2-mercaptoethanol or treatment with boiling water for 5 h. Application of the gold modified monolith in tandem with a packed C18 capillary column is demonstrated with baseline separation of a peptide mixture achieved in a two step process. The first involves retention of cysteine-containing peptides in monolith with reversed phase separation of all other peptides, while the retained peptides are released from monolith and separated in the second step.

Downscaling limits and confinement effects in the miniaturization of porous polymer monoliths in narrow bore capillaries

Monolithic poly(butyl methacrylate-co-ethylene dimethacrylate) columns have been prepared in capillaries ranging in inner diameter from 5 to 75 microm using thermally initiated free-radical polymerization of a mixture of butyl methacrylate, ethylene dimethacrylate, and porogens at different temperatures. Scanning electron microscopy and the measurement of hydrodynamic properties reveal that the downward scalability of the monolithic columns is greatly affected by the confinement effect of the capillary wall resulting from the decreased volume-to-surface ratio as the capillary diameter is decreased. The downscaling process is affected most by the polymerization temperature, the diffusion of the propagating radicals, and the density of coverage of polymerizable groups on the inner walls of the capillary. Optimization of all these factors enables the preparation of monolithic structures in capillaries with inner diameters as low as 5 microm while retaining the desirable properties of monoliths prepared in much larger capillaries. Under these conditions, formation of undesired dense polymer layers attached to the capillary wall was minimized. The chromatographic performance of 10, 25, and 50 microm capillaries evaluated in the reversed phase gradient separation of three proteins showed no change in elution times at identical flow velocities and gradient times, while peak elution width was the smallest with the narrowest capillary.

On-line multi-enzymatic approach for improved sequence coverage in protein analysis

The development of a new mixed bioreactor for proteomic studies based on trypsin and chymotrypsin is described. Trypsin and chymotrypsin were simultaneously bonded to an epoxy monolithic silica column (100 mmx4.6 mm id) in a one-step reaction via epoxy-groups. In order to compare the catalytic properties of the two enzymes in the isolated and in the multi-enzymatic approach, two other single enzyme bioreactors based on trypsin and chymotrypsin were prepared following the same immobilization protocol. The kinetic parameters of the multi-enzymatic bioreactor were derived and it was demonstrated that it retains the individual catalytic activity of the two enzymes. To prove the power of this experimental approach the new mixed bioreactor was integrated in an LC-ESI-MS/MS system for digestion, enrichment, separation and identification of the test protein insulin-like growth factor binding-protein 1 (IGFBP-1). The peptide map and protein sequence coverage obtained with the three bioreactors were compared. The results clearly indicate that the proposed multi-enzyme approach can reduce both digestion and analysis time, accelerate data interpretation and increase the confidence degree in protein identification.