Kinetics of Proteolytic Reactions in Nanoporous Materials

A novel device for swift and efficient CD44 protein digestion of pipette tips in human serum

For molecular diagnostics in modern biomedical research, electrospray ionisation mass spectrometry (ESI-MS) based on proteome profiling is important. Now a days, sample preparation such as proteolysis and protein extraction remain incredibly challenging and inefficient. Recent sample-preparation methods based on micro tips show promising results toward the aim "a proteome in an hour". Proteolysis at the tip, is still infrequently observed and does not represent the processing of complex bio-samples. In this study, we outline a unique technique for detecting and extracting human serum CD44 biomarkers by ligand-protein interactions. This method employs macropores silica particles (MPSP) or (MOSF) modified with hyaluronic acid (HA). In order to assist in the profile of the human serum proteome, we limitations of immunoassays for rapid and multimodal proteolysis. For effective in situ proteolysis, in micropipette tips, MPSP were designed as nanoreactors with variable pore size and surface chemistry. In MS-based bottom-up proteome analysis, the device as-built demonstrated favourable sensitivity (LOD of 0.304 ± 0.007 ng/mL and LOQ of 0.973 ± 0.054 ng/mL), selectivity, durability (at -20 °C for 2 months), reuse (at least 10 times), and minimal memory impact. In addition, we examined into specific surface chemistries of nanoparticles for the absorption of proteins in serum and profiled the HA-binding serum proteome, setting a new preliminary benchmark for future databases. Our study not only helped establish a new platform for extracting/detection of CD44 and identifying the HA-binding proteome, but it also offered design recommendations for ligand affinity-based techniques for the antibody-free study of serum biomarkers with a view towards diagnostic applications.

Rapid sample preparation workflow based on enzymatic nanoreactors for potential serum biomarker discovery in pancreatic cancer

Mass spectrometry (MS)-based proteomics have been extensively applied in clinical practice to discover potential protein and peptide biomarkers. However, the traditional sample pretreatment workflow remains labor-intensive and time-consuming, which limits the application of MS-based proteomic biomarker discovery studies in a high throughput manner. In the current work, we improved the previously reported procedure of the simple and rapid sample preparation methods (RSP) by introducing macroporous ordered siliceous foams (MOSF), namely RSP-MOSF. With the aid of MOSF, we further reduced the digestion time to 10 min, facilitating the whole sample handling process within 30 min. Combining with 30 min direct data independent acquisition (DIA) of LC-MS/MS, we accomplished a serum sample analysis in 1 h. Comparing with the RSP method, the performance of protein and peptide identification, quantitation, as well as the reproducibility of RSP-MOSF is comparable or even outperformed the RSP method. We further applied this workflow to analyze serum samples for potential candidate biomarker discovery of pancreatic cancer. Overall, 576 serum proteins were detected with 41 proteins significantly changed, which could serve as potential biomarkers for pancreatic cancer. Additionally, we evaluated the performance of RSP-MOSF method in a 96-well plate format which demonstrated an excellent reproducibility of the analysis. These results indicated that RSP-MOSF method had the potential to be applied on an automatic platform for further scaled analysis.

Single molecule fluorescence imaging of nanoconfinement in porous materials

This review covers recent progress in using single molecule fluorescence microscopy imaging to understand the nanoconfinement in porous materials. The single molecule approach unveils the static and dynamic heterogeneities from seemingly equal molecules by removing the ensemble averaging effect. Physicochemical processes including mass transport, surface adsorption/desorption, and chemical conversions within the confined space inside porous materials have been studied at nanometer spatial resolution, at the single nanopore level, with millisecond temporal resolution, and under real chemical reaction conditions. Understanding these physicochemical processes provides the ability to quantitatively measure the inhomogeneities of nanoconfinement effects from the confining properties, including morphologies, spatial arrangement, and trapping domains. Prospects and limitations of current single molecule imaging studies on nanoconfinement are also discussed.

Mesoporous Silica as Sorbents and Enzymatic Nanoreactors for Microbial Membrane Proteomics

The membrane proteins of microbes are at the forefront of host and parasite interactions. Having a general view of the functions of microbial membrane proteins is vital for many biomedical studies on microbiota. Nevertheless, due to the strong hydrophobicity and low concentration of membrane proteins, it is hard to efficiently enrich and digest the proteins for mass spectrometry analysis. Herein, we design an enzymatic nanoreactor for the digestion of membrane proteins using methylated well-ordered hexagonal mesoporous silica (Met-SBA-15). The material can efficiently extract hydrophobic membrane proteins and host the proteolysis in nanopores. The performance of the enzymatic nanoreactor is first demonstrated using standard hydrophobic proteins and then validated using membrane proteins extracted from Escherichia coli (E. coli) or a mixed bacterial sample of eight strains. Using the nanoreactor, 431 membrane proteins are identified from E. coli, accounting for 38.5% of all membrane proteins of the species, which is much more than that by the widely used in-solution digestion protocol. From the mixed bacterial sample of eight strains, 1395 membrane proteins are identified using the nanoreactor. On the contrary, the traditional in-solution proteolysis workflow only leads to the identification of 477 membrane proteins, demonstrating that the Met-SBA-15 can be offered as an excellent tool for microbial membrane proteome research and is expected to be used in human microbiota studies, e.g. host-microbe interactions.

Fabrication of a porous polymer membrane enzyme reactor and its enzymatic kinetics study in an artificial kidney model

A porous polymer membrane-based d-amino acid oxidase (DAAO) reactor was developed that mimicked enzymatic activity in a renal ischemia model. Using glycidyl methacrylate as a biocompatible reactive monomer, poly(styrene-glycidyl methacrylate) was synthesized via a reversible addition fragment chain transfer polymerization technique. The prepared porous polymer membrane was used as a support to effectively immobilize DAAO. Compared to DAAO modified on nonporous polymer membrane and free DAAO in solution, the constructed porous polymer membrane-based DAAO enzyme reactor displayed 3-fold and 19-fold increase in enzymolysis efficiency, respectively. In addition, a chiral ligand exchange capillary electrophoresis system for DAAO was used to study DAAO enzymatic kinetics with d,l-methionine as the substrate. The proposed porous polymer membrane-based enzyme reactor showed excellent performance both on reproducibility and stability. Moreover, the enzyme reactor was successfully applied to mimic DAAO activity in a renal ischemia model. These results demonstrated that the enzyme could be efficiently immobilized onto a porous polymer membrane as an enzyme reactor and has great potential in mimicking the enzymatic activity in kidney.

Single Molecule Investigation of Nanoconfinement Hydrophobicity in Heterogeneous Catalysis

Nanoconfinement imposes physical constraints and chemical effects on reactivity in nanoporous catalyst systems. In the present study, we lay the groundwork for quantitative single-molecule measurements of the effects of chemical environment on heterogeneous catalysis in nanoconfinement. Choosing hydrophobicity as an exemplary chemical environmental factor, we compared a range of essential parameters for an oxidation reaction on platinum nanoparticles (NPs) confined in hydrophilic and hydrophobic nanopores. Single-molecule experimental measurements at the single particle level showed higher catalytic activity, stronger adsorption strength, and higher activation energy in hydrophobic nanopores than those in hydrophilic nanopores. Interestingly, different dissociation kinetic behaviors of the product molecules in the two types of nanopores were deduced from the single-molecule imaging data.

Water-in-oil microcompartments for the study of biomimetic drug metabolism

Microcompartments in the form of water-in-oil droplets have been utilized to construct artificial cells and simulate human body environment. However, the performance of subcellular structure involved metabolism in emulsion droplets has not been explored, and the underlying mechanism is still being elucidated. In this work, drug metabolism is presented on the basis of great amounts of microcompartments formed of picoliter-volume droplets with different radius (R), using a commercial four-way valve as a droplet generator. A model substrate, phenacetin, and its metabolite, paracetamol, are quantitatively analyzed by liquid-chromatography (LC) tandem mass spectrometry (MS/MS), and the reaction kinetics is characterized. In microdroplets of varying size (R = 18, 27, 42, and 51 μm, respectively), both conversion ratio and reaction rate constant of the metabolism are influenced in different degree. For instance, the substrate conversion ratio after 60 min of incubation in R = 27 μm droplets improves from 15% to 42%, and the reaction rate constant improves nearly five-fold, compared to that in bulk phase. The influence of microcompartment size on metabolism rate is further explored by simulation using a diffusion-reaction model. The droplet-based strategy is rapid, accurate and cost-efficient, fitting especially into biomimetic metabolism studies.

Deciphering nanoconfinement effects on molecular orientation and reaction intermediate by single molecule imaging

Nanoconfinement could dramatically change molecular transport and reaction kinetics in heterogeneous catalysis. Here we specifically design a core-shell nanocatalyst with aligned linear nanopores for single-molecule studies of the nanoconfinement effects. The quantitative single-molecule measurements reveal unusual lower adsorption strength and higher catalytic activity on the confined metal reaction centres within the nanoporous structure. More surprisingly, the nanoconfinement effects on enhanced catalytic activity are larger for catalysts with longer and narrower nanopores. Experimental evidences, including molecular orientation, activation energy, and intermediate reactive species, have been gathered to provide a molecular level explanation on how the nanoconfinement effects enhance the catalyst activity, which is essential for the rational design of highly-efficient catalysts.

Microwave-Assisted Protein Digestion in a Plate Well for Facile Sampling and Rapid Digestion

Protein digestion is one of the most important processes in proteomic analysis. Here, we report microwave-assisted protein digestion in a plate well, which allows for facile sampling as well as rapid protein digestion based on the combination of highly stable enzyme immobilization and 3D printing technologies. Trypsin (TR) was immobilized on polystyrene-based nanofibers via an enzyme coating (EC) approach. The EC with stabilized TR activity was assembled with the 3D-printed structure in the plate well (EC/3D), which provides two separated compartments for the solution sampling and the TR-catalyzed protein digestion, respectively. EC/3D can effectively prevent the interference of sampling by accommodating EC in the separated compartment from the sampling hole in the middle. EC/3D in the plate well maintained its protein digestion performance under shaking over 160 days. Microwave irradiation enabled the digestion of bovine serum albumin within 10 min, generating the MALDI-TOF MS results of 75.0% sequence coverage and 61 identified peptides. EC/3D maintained its protein digestion performance under microwave irradiation after 30 times of recycled uses. EC/3D in the plate well has demonstrated its potential as a robust and facile tool for the development of an automated protein digestion platform. The combination of stable immobilized enzymes and 3D-printed structures can be potentially utilized not only for the protein digestion, but also for many other enzyme applications, including bioconversion and biosensors.

Polydopamine Grafted Porous Graphene as Biocompatible Nanoreactor for Efficient Identification of Membrane Proteins

Functional nanomaterials, used as nanoreactors, have shown great advantages in a variety of applications in biomedical fields. Herein, we designed a novel nanoreactor system toward the application in membrane proteomics by using polydopamine-coated nanoporous graphene foams (NGFs-PD) prepared by a facile in situ oxidative polymerization. Taking advantage of the unique 3-D structure and surface functionalization, NGFs-PD can quickly adsorb a large amount of hydrophobic membrane proteins dissolved in sodium dodecyl sulfonate (SDS)/methanol and hydrophilic trypsin in aqueous solution, and then confine the proteolysis in the nanoscale domains to fasten the reaction rate. Therefore, the current nanoreactor system combines the multifunctions of highly efficient solubilization, immobilization, and proteolysis of membrane proteins. With the nanoreactor, digestion of standard membrane proteins can be finished in 10 min. 893 membrane proteins were identified from human glioma cells (U251). All these superiorities indicate that the biocompatible NGFs-PD nanoreactor system is of great promise to facilitate high-throughput membrane proteomic analysis.

Porous silica enhanced proteolysis during Off-Gel separation for efficient protein identification

An advanced approach is developed in this work for simultaneous on-line separation and digestion of proteins by combining the Off-Gel isoelectric focusing (IEF) and enzymatic nanoreactor enhanced proteolysis. The nanoreactor was prepared by preloading trypsin in amino-functionalized macroporous silica, and then directly added into Off-Gel wells. With the nanoreactor loaded Off-Gel device, effective digestion of proteins happened during IEF electrophoresis to generate directly fractionated tryptic peptides, which not only accelerated the experimental flow but also avoided sample loss, leading to a more comprehensive protein identification from complex biological samples. A successful identification of 3592 proteins was achieved from Hela cell line by using the approach followed with LC-MS/MS analysis, while only 1877 proteins were identified from the same sample when using standard in-solution proteolysis followed with Off-Gel electrophoresis and then LC-MS/MS analysis. Therefore, we have demonstrated that the approach can greatly simplify high-throughput proteomics and significantly improve protein identification.

Multifunctional nanoreactor for comprehensive characterization of membrane proteins based on surface functionalized mesoporous foams

An integrated protocol is proposed here for efficient analysis of membrane proteins based on surface functionalized mesoporous graphene foams (MGF). The inherent hydrophobic nature of MGF and surface modification with hydrophilic chitosan (CS) make it highly suitable for the enrichment of hydrophobic membrane proteins from organic solvent, while remaining well-dispersed in aqueous solution for subsequent proteolysis. Therefore, such a multifunctional reactor ensures a facile solvent adjustment route. Furthermore, as a chitosan modified nanoporous reactor, it also provides a biocompatible nanoenvironment that can maintain the stability and activity of enzymes to realize efficient in situ digestion of the enriched membrane proteins. The concept was first proved with a standard hydrophobic membrane protein, bacteriorhodopsin, where a high number of identified peptides and amino acid sequence coverage were achieved even at extremely low protein concentration. The mesoporous reaction system was further applied to the analysis of complex real-case proteome samples, where 931 membrane proteins were identified in triplicate analyses by 2D LC-MS/MS. In contrast, with in-solution proteolysis, only 73 membrane proteins were identified from the same sample by the same 2D LC-MS/MS. The identified membrane proteins by the MGF-CS protocol include many biomarkers of the cell line. These results suggest that the multifunctional MGF-CS protocol is of great value to facilitate the comprehensive characterization of membrane proteins in the proteome research.

High-efficiency nano/micro-reactors for protein analysis

This article reviews the recent advances regarding the development of nanomaterial-based nanoreactors and microfluidic droplet reactors and their applications in protein analysis.

Poly(2-vinyl-4,4-dimethylazlactone)-functionalized magnetic nanoparticles as carriers for enzyme immobilization and its application

Fabrication of various efficient enzyme reactors has triggered increasing interests for its extensive applications in biological and clinical research. In this study, magnetic nanoparticles were functionalized by a biocompatible reactive polymer, poly(2-vinyl-4,4-dimethylazlactone), which was synthesized by reversible addition-fragmentation chain transfer polymerization. Then, the prepared polymer-modified magnetic nanoparticles were employed as favorable carriers for enzyme immobilization. l-Asparaginase was selected as the model enzyme to fabricate the enzyme reactor, and the prepared enzyme reactor exhibited high loading capacity of 318.0 μg mg(-1) magnetic nanoparticle. Interestingly, it has been observed that the enzymolysis efficiency increased slightly with the lengthened polymer chain, resulting from the increased immobilization amount of enzyme. Meanwhile, the immobilized enzyme could retain more than 95.7% activity after 10 repeated uses and maintain more than 72.6% activity after 10 weeks storage. Moreover, an extracorporeal shunt system was simulated to estimate the potential application capability of the prepared l-asparaginase reactor in acute lymphoblastic leukemia treatment.

Construction of a D-amino acid oxidase reactor based on magnetic nanoparticles modified by a reactive polymer and its application in screening enzyme inhibitors

Developing facile and high-throughput methods for exploring pharmacological inhibitors of D-amino acid oxidase (DAAO) has triggered increasing interest. In this work, DAAO was immobilized on the magnetic nanoparticles, which were modified by a biocompatible reactive polymer, poly(glycidyl methacrylate) (PGMA) via an atom transfer radical polymerization technique. Interestingly, the enzyme immobilization process was greatly promoted with the assistance of a lithium perchlorate catalyst. Meanwhile, a new amino acid ionic liquid (AAIL) was successfully synthesized and employed as the efficient chiral ligand in a chiral ligand exchange capillary electrophoresis (CLE-CE) system for chiral separation of amino acids (AAs) and quantitation of methionine, which was selected as the substrate of DAAO. Then, the apparent Michaelis-Menten constants in the enzyme system were determined with the proposed CLE-CE method. The prepared DAAO-PGMA-Fe3O4 nanoparticles exhibited excellent reusability and good stability. Moreover, the enzyme reactor was successfully applied in screening DAAO inhibitors. These results demonstrated that the enzyme could be efficiently immobilized on the polymer-grafted magnetic nanoparticles and that the obtained enzyme reactor has great potential in screening enzyme inhibitors, further offering new insight into monitoring the relevant diseases.

A combo-pore approach for the programmable extraction of peptides/proteins

A novel combo-pore approach has been designed for the programmable purification, minimisation of sample complexity, enrichment and sensitive detection of peptides in biosamples. This approach has a superior performance to conventional protocols and commercial products.

Sensitive assay of protease activity on a micro/nanofluidics preconcentrator fused with the fluorescence resonance energy transfer detection technique

A fast and sensitive assay of protease activity on a micro/nanofluidics preconcentrator combining with fluorescence resonance energy transfer (FRET) detection technique has been developed in a homogeneous real-time format. First, the functionalized nanoprobes are formed by loading dye labeled protein onto gold nanoparticles (AuNPs), in which, the photoluminescence of donor dye was strongly quenched by AuNPs due to FRET mechanisms. For protease activity assay, the nanoprobes are enriched by a micro/nanofluidics preconcentrator. When the target protease is transported to the enriched nanoprobes, cleavage of protein occurs as a consequence of molecular recognition of enzyme to substrate. The release of cleavage fragments from AuNPs nanoprobes leads to the enhancement of fluorescence and enables the protease activity assay on the micro/nanofluidics chip. As a demonstration, digestion of fluorescein isothiocyanate labeled dog serum albumin (FITC-DSA) by trypsin was used as a model reaction. Because of the highly efficient preconcentration and space confinement effect, significantly increased protein cleavage rate and protease assay sensitivity can be achieved with enhanced enzyme activity. The present micro/nanofluidics platform fused with the FRET detection technique is promising for fast and sensitive bioanalysis such as immunoassay, DNA hybridization, drug discovery, and clinical diagnosis.

Applications of nanomaterials in mass spectrometry analysis

Mass spectrometry (MS) based analyses have received intense research interest in a series of rapidly developing disciplines. Although current MS techniques have enjoyed great successes, several key challenges still remain in practical applications, especially for the detection of biomolecules in biological systems. The use of nanomaterials in MS based analysis provides a promising approach due to their unique physical and chemical properties. In this review, nanomaterials with different compositions and nanostructures employed in MS applications are summarised and classified by their functions. Such an integrated and wide reaching review will provide a comprehensive handbook to researchers with various backgrounds working in this exciting interdisciplinary area.

Electrostatic control of peptide side-chain reactivity using amphiphilic homopolymer-based supramolecular assemblies

Supramolecular assemblies formed by amphiphilic homopolymers with negatively charged groups in the hydrophilic segment have been designed to enable high labeling selectivity toward reactive side chain functional groups in peptides. The negatively charged interiors of the supramolecular assemblies are found to block the reactivity of protonated amines that would otherwise be reactive in aqueous solution, while maintaining the reactivity of nonprotonated amines. Simple changes to the pH of the assemblies' interiors allow control over the reactivity of different functional groups in a manner that is dependent on the pKa of a given peptide functional group. The labeling studies carried out in positively charged supramolecular assemblies and free buffer solution show that, even when the amine is protonated, labeling selectivity exists only when complementary electrostatic interactions are present, thereby demonstrating the electrostatically controlled nature of these reactions.

Capillary electrophoretic enzyme assays

In the past years, capillary electrophoresis has become a frequently used technique for enzyme assays due to the high separation efficiency and versatility as well as small sample size and low consumption of chemicals. The capillary electrophoresis assays can be divided into two general categories: pre-capillary (or offline) assays and in-capillary (or online) assays. In pre-capillary assays, the incubation is performed offline and substrate(s) and product(s) are subsequently analyzed by capillary electrophoresis. In in-capillary assays enzyme reaction and separation of the analytes are performed inside the same capillary. In such assays the enzyme is either immobilized or in solution. The latter techniques is also referred to as electrophoretically mediated microanalysis (EMMA) indicating that the individual steps of the incubation as well as analysis are performed via electrophoretic phenomena. This chapter describes both techniques using the deacetylation of acetyl-lysine residues in model peptides by sirtuin enzymes as well as the hydrolysis of acetylthiocholine by acetylcholinesterase as examples.

Limited proteolysis via millisecond digestions in protease-modified membranes

Sequential adsorption of poly(styrene sulfonate) (PSS) and proteases in porous nylon yields enzymatic membrane reactors for limited protein digestion. Although a high local enzyme density (~30 mg/cm(3)) and small pore diameters in the membrane lead to digestion in <1 s, the low membrane thickness (170 μm) affords control over residence times at the millisecond level to limit digestion. Apomyoglobin digestion demonstrates that peptide lengths increase as the residence time in the membrane decreases. Moreover, electron transfer dissociation (ETD) tandem mass spectrometry (MS/MS) on a large myoglobin proteolytic peptide (8 kDa) provides a resolution of 1-2 amino acids. Under denaturing conditions, limited membrane digestion of bovine serum albumin (BSA) and subsequent ESI-Orbitrap MS analysis reveal large peptides (3-10 kDa) that increase the sequence coverage from 53% (2 s digestion) to 82% (0.05 s digestion). With this approach, we also performed membrane-based limited proteolysis of a large Arabidopsis GTPase, Root Hair Defective 3 (RHD3) and showed suitable probing for labile regions near the C-terminus to suggest what protein reconstruction might make RHD3 more suitable for crystallization.

Periodic mesoporous organosilica as a multifunctional nanodevice for large-scale characterization of membrane proteins

A versatile protocol has been developed for large-scale characterization of hydrophobic membrane proteins based on the periodic mesoporous organosilica (PMO) acting as both an extractor for hydrophobic substrate capture and a nanoreactor for efficient in situ digestion. With introduction of organic groups in the pore frameworks and the presence of hydrophilic silanol groups on the surface, PMO can be well-dispersed into not only an organic solution to concentrate the dissolved membrane proteins but also an aqueous solution containing enzymes for sequential rapid proteolysis in the nanopores. The unique amphiphilic property of PMO ensures a facile switch in different solutions to realize the processes of substrate dissolution, enrichment, and digestion effectively. Furthermore, this novel PMO-assisted protocol has been successfully applied for identification of complex membrane proteins extracted from mouse liver as proof of general applicability.

In mesopore protein digestion: a new forthcoming strategy in proteomics

The conventional protocols for in solution or in gel protein digestion require many steps and long reaction times. The use of trypsin immobilized onto solid supports has recently captured the attention of many research groups, because these systems can speed-up protein digestion significantly. The utilization of new materials such as mesoporous silica as supports, in which enzyme and substrate are dramatically concentrated and confined in the nanospace, offers new opportunities to reduce the complexity of proteomics workflows. An overview of the procedures for in situ proteolysis of single proteins or complex protein mixtures is reported, with a special focus on porous materials used as catalysts. The challenging efforts for designing such systems aimed at mimicking the biochemistry of living cells are reviewed. Potentials, limitations and challenges of this branch of enzyme catalysis, which we indicate as in mesopore digestion, are discussed, in relation to its suitability for high-speed and high-throughput proteomics.

Facile trypsin immobilization in polymeric membranes for rapid, efficient protein digestion

Sequential adsorption of poly(styrene sulfonate) and trypsin in nylon membranes provides a simple, inexpensive method to create stable, microporous reactors for fast protein digestion. The high local trypsin concentration and short radial diffusion distances in membrane pores facilitate proteolysis in residence times of a few seconds, and the minimal pressure drop across the thin membranes allows their use in syringe filters. Membrane digestion and subsequent MS analysis of bovine serum albumin provide 84% sequence coverage, which is higher than the 71% coverage obtained with in-solution digestion for 16 h or the <50% sequence coverages of other methods that employ immobilized trypsin. Moreover, trypsin-modified membranes digest protein in the presence of 0.05 wt % sodium dodecyl sulfate (SDS), whereas in-solution digestion under similar conditions yields no peptide signals in mass spectra even after removal of SDS. These membrane reactors, which can be easily prepared in any laboratory, have a shelf life of several months and continuously digest protein for at least 33 h without significant loss of activity.

Nanomaterial-assisted laser desorption ionization for mass spectrometry-based biomedical analysis

Nanomaterials have been widely used to assist laser desorption ionization of biomolecules for mass spectrometry analysis. Compared with classical matrix-assisted laser desorption ionization, strategies based on nanomaterial-assisted ionization generate a clean background, which is of great benefit for the qualitative and quantitative analysis of small biomolecules, such as therapeutic and diagnostic molecules. As label-free platforms, they have successfully been used for high-throughput enzyme activity/inhibition monitoring and also for tissue imaging to map in situ the distribution of peptides, metabolites and drugs. In addition to widely used porous silicon nanomaterials, gold nanoparticles can be easily chemically modified by thiol-containing compounds, opening novel interesting perspectives. Such functionalized nanoparticles have been used both as probes to extract target molecules and as matrices to assist laser desorption ionization for developing new enzyme immunoassays or for studying DNA hybridization. More recently, semiconductor nanomaterials or quantum dots acting as photosensitive centers to induce in-source redox reactions for proteomics and to investigate biomolecule oxidation for metabolomics have been shown to offer new analytical strategies.

Recent advances in proteolysis and peptide/protein separation by chromatographic strategies

This review gives a broad glance on the progress of recent advances on proteolysis and peptide/protein separation by chromatographic strategies in the past ten years, covering the main research in these areas especially in China. The reviewed research focused on enzymatic micro-reactors and peptide separation in bottom-up approaches, and protein and peptide separation in top-down approaches. The new enzymatic micro-reactor is able to accelerate proteolytic reaction rate from conventionally a couple of hours to a few seconds, and the multiple dimensional chromatographic-separation with various models or arrays could sufficiently separate the proteomic mixture. These advances have significantly promoted the research of protein/peptide separation and identification in proteomics.

Functionalized periodic mesoporous organosilicas for enhanced and selective peptide enrichment

The analysis of peptides by the mass spectrometry (MS) technique is important in modern life science. The enrichment of peptides can increase the detection efficiency and is sometimes indispensable for collecting the information on proteins with low-abundance. Herein, we first report that functionalized periodic mesoporous organosilica (PMO) materials have a superior peptide enrichment property. It is demonstrated that the PMO materials with an organo-bridged (-CH(2)-) hybrid wall composition display a highly enhanced peptide enrichment ability compared to the pure silica material (SBA-15) with similar mesostructured parameters and morphology. More importantly, by surface modification of PMO with amino groups (denoted NH(2)-PMO), PMO and NH(2)-PMO with opposite charged surfaces (-25.2 and +39.0 mV, respectively) show selective affinities for positively and negatively charged peptides, respectively. By directly adding PMO, NH(2)-PMO as well as pure silica materials to the peptides solution with a low concentration (1-2 fmol/microL), 36 and 28 peptides can be detected from the BSA digestion in the presence of PMO and NH(2)-PMO, respectively, while only 6 and 4 are monitored in the case of SBA-15 enrichment and from solution without enrichment, respectively. Moreover, 69.4% (25 of 36) of enriched peptides by PMO have pI > or = 6 and 80% (21 of 28) of enriched peptides by NH(2)-PMO possess pI < or = 6. Combining the results from the NH(2)-PMO and PMO enrichment together, 51 peptides can be identified with a MOWSE score of 333. It is also noted that similar conclusions can also be obtained from the peptides solution originated from other proteins. This might be an important contribution to the understanding of the interaction between peptides and porous hosts, and the proposed method is promising for the development of both material science and biotechnology.

Advances in capillary electrophoretic enzyme assays

In recent years, capillary electrophoresis (CE) has become a frequently used tool for enzyme assays due to its well-recognized advantages such as high separation efficiency, short analysis time, small sample and chemicals consumption. The published applications cover all aspects of enzyme characterization and analysis including the determination of the enzyme activity, substrate and modulator characterization and identification, as well as the investigation of enzyme-mediated metabolic pathways of bioactive molecules. The CE assays may be classified into two general categories: (1) pre-capillary assays where the reactions are performed offline followed by CE analysis of the substrates and products and (2) online assays when the enzyme reaction and separation of the analytes are performed in the same capillary. In online assays, the enzyme may be either immobilized or in solution. The latter is also referred to as electrophoretically mediated microanalysis (EMMA). The present review will highlight the literature of CE-based enzyme assays from 2006 to November 2009. One section will be devoted to applications of microfluidic devices.