Gold Nanoparticle Assembly Microfluidic Reactor for Efficient On-line Proteolysis

The Fabrication and Bonding of Thermoplastic Microfluidics: A Review

Various fields within biomedical engineering have been afforded rapid scientific advancement through the incorporation of microfluidics. As literature surrounding biological systems become more comprehensive and many microfluidic platforms show potential for commercialization, the development of representative fluidic systems has become more intricate. This has brought increased scrutiny of the material properties of microfluidic substrates. Thermoplastics have been highlighted as a promising material, given their material adaptability and commercial compatibility. This review provides a comprehensive discussion surrounding recent developments pertaining to thermoplastic microfluidic device fabrication. Existing and emerging approaches related to both microchannel fabrication and device assembly are highlighted, with consideration toward how specific approaches induce physical and/or chemical properties that are optimally suited for relevant real-world applications.

Bio-functionalization of microfluidic platforms made of thermoplastic materials: A review

As a result of their favorable physical and chemical characteristics, thermoplastics have garnered significant interest in the area of microfluidics. The moldable nature of these inexpensive polymers enables easy fabrication, while their durability and chemical stability allow for resistance to high shear stress conditions and functionalization, respectively. This review provides a comprehensive examination several commonly used thermoplastic polymers in the microfluidics space including poly(methyl methacrylate) (PMMA), cyclic olefin polymer (COP) and copolymer (COC), polycarbonates (PC), poly(ethylene terephthalate) (PET), polystyrene (PS), poly(ethylene glycol) (PEG), polylactic acid (PLA), acrylonitrile butadiene styrene (ABS), and polyester. We describe various biofunctionalization strategies applied within thermoplastic microfluidic platforms and their resultant applications. Lastly, emerging technologies with a focus on applying recently developed microfluidic and biofunctionalization strategies into thermoplastic systems are discussed.

Construction of a microfluidic platform integrating online protein fractionation, denaturation, digestion, and peptide enrichment

Microfluidic system with multi-functional integration of high-throughput protein/peptide separation ability has great potential for improving the identification capacity of biological samples in proteomics. In this paper, a sample treatment platform was constructed by integrating reversed phase chromatography, immobilized enzyme reactor (IMER) and imprinted monolith through a microfluidic chip to achieve the online proteins fractionation, denaturation, digestion and peptides enrichment. We firstly synthesized a poly-allyl phenoxyacetate (AP) monolith and a lysine-glycine-glycine (KGG) imprinted monolith separately, and investigated in detail their performance in fractionating proteins and extracting KGG from the protein digests of MCF-7 cell. The removal percentage of 94.6% for MCF-7 cell protein and the recovery of 90.8% for KGG were obtained. The number of proteins and peptides identified on this microfluidic platform was 2,004 and 8,797, respectively, which was 2.8-fold and 3.0-fold higher than that of untreatment sample. The time consumed by this platform for a sample treatment was about 9.6 h, less than that of conventional method (approximate 13.3 h). In addition, this platform can enrich some peptide fragments containing KGG based on imprinted monolith, which can be served for the identification of ubiquitin-modified proteomics. The successful construction of this integrated microfluidic platform provides a considerable and efficient technical tool for simultaneous identification of proteomics and post-translational modification proteomics information.

Fast Enzymatic Processing of Proteins for MS Detection with a Flow-through Microreactor

The vast majority of mass spectrometry (MS)-based protein analysis methods involve an enzymatic digestion step prior to detection, typically with trypsin. This step is necessary for the generation of small molecular weight peptides, generally with MW < 3,000-4,000 Da, that fall within the effective scan range of mass spectrometry instrumentation. Conventional protocols involve O/N enzymatic digestion at 37 ºC. Recent advances have led to the development of a variety of strategies, typically involving the use of a microreactor with immobilized enzymes or of a range of complementary physical processes that reduce the time necessary for proteolytic digestion to a few minutes (e.g., microwave or high-pressure). In this work, we describe a simple and cost-effective approach that can be implemented in any laboratory for achieving fast enzymatic digestion of a protein. The protein (or protein mixture) is adsorbed on C18-bonded reversed-phase high performance liquid chromatography (HPLC) silica particles preloaded in a capillary column, and trypsin in aqueous buffer is infused over the particles for a short period of time. To enable on-line MS detection, the tryptic peptides are eluted with a solvent system with increased organic content directly in the MS ion source. This approach avoids the use of high-priced immobilized enzyme particles and does not necessitate any aid for completing the process. Protein digestion and complete sample analysis can be accomplished in less than ~3 min and ~30 min, respectively.

Proteolytic Digestion and TiO2 Phosphopeptide Enrichment Microreactor for Fast MS Identification of Proteins

The characterization of phosphorylation state(s) of a protein is best accomplished by using isolated or enriched phosphoprotein samples or their corresponding phosphopeptides. The process is typically time-consuming as, often, a combination of analytical approaches must be used. To facilitate throughput in the study of phosphoproteins, a microreactor that enables a novel strategy for performing fast proteolytic digestion and selective phosphopeptide enrichment was developed. The microreactor was fabricated using 100 μm i.d. fused-silica capillaries packed with 1-2 mm beds of C18 and/or TiO2 particles. Proteolytic digestion-only, phosphopeptide enrichment-only, and sequential proteolytic digestion/phosphopeptide enrichment microreactors were developed and tested with standard protein mixtures. The protein samples were adsorbed on the C18 particles, quickly digested with a proteolytic enzyme infused over the adsorbed proteins, and further eluted onto the TiO2 microreactor for enrichment in phosphopeptides. A number of parameters were optimized to speed up the digestion and enrichments processes, including microreactor dimensions, sample concentrations, digestion time, flow rates, buffer compositions, and pH. The effective time for the steps of proteolytic digestion and enrichment was less than 5 min. For simple samples, such as standard protein mixtures, this approach provided equivalent or better results than conventional bench-top methods, in terms of both enzymatic digestion and selectivity. Analysis times and reagent costs were reduced ~10- to 15-fold. Preliminary analysis of cell extracts and recombinant proteins indicated the feasibility of integration of these microreactors in more advanced workflows amenable for handling real-world biological samples. Graphical Abstract ᅟ.

Beyond classical derivatization: analyte ‘derivatives’ in the bioanalysis of endogenous and exogenous compounds

The analysis of endogenous and exogenous analytes in biological matrices presents several challenges to the bioanalyst. These analytes are often present at low concentrations, typically in complex matrices, and may have physicochemical properties that are not amenable to LC–MS analysis. The bioanalyst thus relies heavily on the formation of analyte derivatives for the efficient quantification of these compounds. These derivatives are also critically employed to derive information on the biology of living systems, potential drug or disease targets, and biomarkers of drug efficacy, safety, or disease progression. In this perspective, we demonstrate how analyte derivatives are applied in modern bioanalytical workflows and we discuss the potential use of these derivatives in the future.

Boronate affinity materials for separation and molecular recognition: structure, properties and applications

Boronate affinity materials, as unique sorbents, have emerged as important media for the selective separation and molecular recognition of cis-diol-containing compounds. With the introduction of boronic acid functionality, boronate affinity materials exhibit several significant advantages, including broad-spectrum selectivity, reversible covalent binding, pH-controlled capture/release, fast association/desorption kinetics, and good compatibility with mass spectrometry. Because cis-diol-containing biomolecules, including nucleosides, saccharides, glycans, glycoproteins and so on, are the important targets in current research frontiers such as metabolomics, glycomics and proteomics, boronate affinity materials have gained rapid development and found increasing applications in the last decade. In this review, we critically survey recent advances in boronate affinity materials. We focus on fundamental considerations as well as important progress and new boronate affinity materials reported in the last decade. We particularly discuss on the effects of the structure of boronate ligands and supporting materials on the properties of boronate affinity materials, such as binding pH, affinity, selectivity, binding capacity, tolerance for interference and so on. A variety of promising applications, including affinity separation, proteomics, metabolomics, disease diagnostics and aptamer selection, are introduced with main emphasis on how boronate affinity materials can solve the issues in the applications and what merits boronate affinity materials can provide.

Optimization of amine-rich multilayer thin films for the capture and quantification of prostate-specific antigen

It is demonstrated that poly(allylamine hydrochloride)/poly(styrenesulfonate) (PAH/SPS) multilayer films can be successfully tailored for the capture and detection of small biomolecules in dilute concentrations. Based on in vitro results, these films could be potentially applied for rapid and high-throughput diagnosis of dilute biomarkers in serum or tissue. PAH presents functional amino groups that can be further reacted with desired chemistries in order to create customizable and specific surfaces for biomolecule capture. A variety of film assembly characteristics were tested (pH, molecular weight of PAH, and ionic strength) to tune the biotinylation and swelling behavior of these films to maximize detection capabilities. The resultant optimized biotinylated PAH/SPS 9.3/9.3 system was utilized in conjunction with quantum dots (Qdots) to capture and detect a dilute biomarker for prostate cancer, prostate-specific antigen (PSA). Compared to previous work, our system presents a good sensitivity for PSA detection within the clinically relevant range of 0.4-100 ng/mL.

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.

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.

Tailoring of a TiO2 nanotube array-integrated portable microdevice for efficient on-chip enrichment and isotope labeling of serum phosphopeptides

Herein we present a gravity-driven microdevice furnished with tunable TiO2 nanotube arrays (TNAs) inside as the separation medium for consecutive on-chip enrichment and isotope labeling of serum phosphopeptides. The 3D tubular architectures of TNAs dramatically enhanced the affinity towards phosphate-containing molecules and also provided a spacious microenvironment for isotope dimethyl labeling reactions. To maximize the efficiency and capacity of the phosphopeptide enrichment, nanoscale tailoring and microscale fabrication were employed for adjusting the TNAs' pore sizes and the channel patterns. The S-shaped microdevice equipped with interior TNAs anodized at 25 V was utilised for consecutive serum processing, and further differential expression analysis of endogenous phosphopeptides between ovarian cancer patients and healthy women. The phosphorylated fibrinogen peptide A (FPA, AD[pS]GEGDFLAEGGGVR) was found to be down-regulated by about 4 times while its isoform (D[pS]GEGDFLAEGGGV) was 2.4-fold up-regulated in the patient specimens. In principle, this nanostructure-embedded model introduced tailor-made bioseparation materials into the microdevice, undoubtedly facilitating the workflow of sample pretreatment and thus assisting the analysis of disease-associated biomolecules in biomedical research.

Proteolysis in microfluidic droplets: an approach to interface protein separation and peptide mass spectrometry

A versatile microreactor protocol based on microfluidic droplets has been developed for on-line protein digestion. Proteins separated by liquid chromatography are fractionated in water-in-oil droplets and digested in sequence. The microfluidic reactor acts also as an electrospray ionization emitter for mass spectrometry analysis of the peptides produced in the individual droplets. Each droplet is an enzymatic micro-reaction unit with efficient proteolysis due to rapid mixing, enhanced mass transfer and automated handling. This droplet approach eliminates sample loss, cross-contamination, non-specific absorption and memory effect. A protein mixture was successfully identified using the droplet-based micro-reactor as interface between reverse phase liquid chromatography and mass spectrometry.

Bioconjugation of trypsin onto gold nanoparticles: effect of surface chemistry on bioactivity

The systematic study of activity, long-time stability and auto-digestion of trypsin immobilized onto gold nanoparticles (GNPs) is described in this paper and compared to trypsin in-solution. Thereby, the influence of GNP's size and immobilization chemistry by various linkers differing in lipophilicity/hydrophilicity and spacer lengths was investigated with regard to the bioactivity of the conjugated enzyme. GNPs with different sizes were prepared by reduction and simultaneous stabilization with trisodium citrate and characterized by UV/vis spectra, dynamic light scattering (DLS), ζ-potential measurements and transmission electron microscopy (TEM). GNPs were derivatized by self-assembling of bifunctional thiol reagents on the nanoparticle (NP) surface via dative thiol-gold bond yielding a carboxylic acid functionalized surface. Trypsin was either attached directly via hydrophobic and ionic interactions onto the citrate stabilized GNPs or immobilized via EDC/NHS bioconjugation onto the carboxylic functionalized GNPs, respectively. The amount of bound trypsin was quantified by measuring the absorbance at 280 nm. The activity of bound enzyme and its Michaelis Menten kinetic parameter K(m) and v(max) were measured by the standard chromogenic substrate N(α)-Benzoyl-DL-arginine 4-nitroanilide hydrochloride (BApNA). Finally, digestion of a standard protein mixture with the trypsin-conjugated NPs followed by analysis with LC-ESI-MS and successful MASCOT search demonstrated the applicability of the new heterogenous nano-structured biocatalyst. It could be shown that the amount of immobilized trypsin and its activity can be increased by a factor of 6 using a long hydrophilic spacer with simultaneous reduced auto-digestion and reduced digestion time. The applicability of the new trypsin bioreactor was proven by digestion of casein and identification of α- as well as κ-casein by subsequent MASCOT search.

Nanomaterials and lab-on-a-chip technologies

Lab-on-a-chip (LOC) platforms have become important tools for sample analysis and treatment with interest for DNA, protein and cells studies or diagnostics due to benefits such as the reduced sample volume, low cost, portability and the possibility to build new analytical devices or be integrated into conventional ones. These platforms have advantages of a wide set of nanomaterials (NM) (i.e. nanoparticles, quantum dots, nanowires, graphene etc.) and offer excellent improvement in properties for many applications (i.e. detectors sensitivity enhancement, biolabelling capability along with other in-chip applications related to the specificities of the variety of nanomaterials with optical, electrical and/or mechanical properties). This review covers the last trends in the use of nanomaterials in microfluidic systems and the related advantages in analytical and bioanalytical applications. In addition to the applications of nanomaterials in LOCs, we also discuss the employment of such devices for the production and characterization of nanomaterials. Both framed platforms, NMs based LOCs and LOCs for NMs production and characterization, represent promising alternatives to generate new nanotechnology tools for point-of-care diagnostics, drug delivery and nanotoxicology applications.

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.

Layer-by-layer deposition of all-nanoparticle multilayers in confined geometries

Nanofluidic arrays containing high-aspect-ratio nanochannels were used as a platform for the deposition of all nanoparticle multilayers. LbL assembly of 6 nm titania and 15 nm silica nanoparticles resulted in conformal multilayers of uniform thickness throughout the nanochannels. These multilayers are inherently nanoporous with void volume fractions of about 0.5. Compared to unconfined assembly of the same materials on flat substrates, thinner multilayer films were observed for the case of deposition within confined channel geometries because of surface charge-induced electrostatic depletion of the depositing species. Additionally, systematic and reproducible bridging of the nanochannels occurred as multilayer assembly progressed, a phenomenon not seen in our earlier work involving polyelectrolytes. This behavior was attributed to relatively weak nanoparticle adsorption and the resulting formation of large aggregates. These results demonstrate a new route by which confined geometries can be coated and even bridged with a nanoporous multilayer without the need for calcination or other postassembly steps to introduce porosity into the conformal coating.

Proteomic reactors and their applications in biology

Proteomic analysis requires the combination of an extensive suite of technologies including protein processing and separation, micro-flow HPLC, MS and bioinformatics. Although proteomic technologies are still in flux, approaches that bypass gel electrophoresis (gel-free approaches) are dominating the field of proteomics. Along with the development of gel-free proteomics, came the development of devices for the processing of proteomic samples termed proteomic reactors. These microfluidic devices provide rapid, robust and efficient pre-MS sample procession by performing protein sample preparation/concentration, digestion and peptide fractionation. The proteomic reactor has advanced in two major directions: immobilized enzyme reactor and ion exchange-based proteomic reactor. This review summarizes the technical developments and biological applications of the proteomic reactor over the last decade.

Development of a multiplexed microfluidic proteomic reactor and its application for studying protein-protein interactions

Mass spectrometry-based proteomics techniques have been very successful for the identification and study of protein-protein interactions. Typically, immunopurification of protein complexes is conducted, followed by protein separation by gel electrophoresis and in-gel protein digestion, and finally, mass spectrometry is performed to identify the interacting partners. However, the manual processing of the samples is time-consuming and error-prone. Here, we developed a polymer-based microfluidic proteomic reactor aimed at the parallel analysis of minute amounts of protein samples obtained from immunoprecipitation. The design of the proteomic reactor allows for the simultaneous processing of multiple samples on the same devices. Each proteomic reactor on the device consists of SCX beads packed and restricted into a 1 cm microchannel by two integrated pillar frits. The device is fabricated using a combination of low-cost hard cyclic olefin copolymer thermoplastic and elastomeric thermoplastic materials (styrene/(ethylene/butylenes)/styrene) using rapid hot-embossing replication techniques with a polymer-based stamp. Three immunopurified protein samples are simultaneously captured, reduced, alkylated, and digested on the device within 2-3 h instead of the days required for the conventional protein-protein interaction studies. The limit of detection of the microfluidic proteomic reactor was shown to be lower than 2 ng of protein. Furthermore, the application of the microfluidic proteomic reactor was demonstrated for the simultaneous processing of the interactome of the histone variant Htz1 in wild-type yeast and in a swr1Δ yeast strain compared to an untagged control using a novel three-channel microfluidic proteomic reactor.

Improvement of proteolytic efficiency towards low-level proteins by an antifouling surface of alumina gel in a microchannel

A microfluidic reactor has been developed for rapid enhancement of protein digestion by constructing an alumina network within a poly(ethylene terephthalate) (PET) microchannel. Trypsin is stably immobilized in a sol-gel network on the PET channel surface after pretreatment, which produces a protein-resistant interface to reduce memory effects, as characterized by X-ray fluorescence spectrometry and electroosmotic flow. The gel-derived network within a microchannel provides a large surface-to-volume ratio stationary phase for highly efficient proteolysis of proteins existing both at a low level and in complex extracts. The maximum reaction rate of the encapsulated trypsin reactor, measured by kinetic analysis, is much faster than in bulk solution. Due to the microscopic confinement effect, high levels of enzyme entrapment and the biocompatible microenvironment provided by the alumina gel network, the low-level proteins can be efficiently digested using such a microreactor within a very short residence time of a few seconds. The on-chip microreactor is further applied to the identification of a mixture of proteins extracted from normal mouse liver cytoplasm sample via integration with 2D-LC-ESI-MS/MS to show its potential application for large-scale protein identification.

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.

A phospho-directed macroporous alumina-silica nanoreactor with multi-functions

A phospho-directed nanoreactor with multiple functions is reported. Alumina-functionalized macroporous ordered silica foams (Al-MOSF) have been developed with large pore size, high pore volume (1.6 cm(3)/g), and a surface area of 186 m(2)/g rich in coordination unsaturated Al species, which can be used as phospho-directed nanoreactors for integrated in situ digestion and in situ phosphoisolation. By directly adding Al-MOSF to the conventional in-solution digestion system, both enzymes and proteins are quickly enriched in the macropores of the reactor to achieve a fast proteolysis without increasing the enzyme/protein concentration or using a preimmobilization process, thus the digestion time and the cost can be greatly reduced. Meanwhile, due to the chemo-affinity between alumina and phosphor groups, the Al-MOSF reactor can in situ isolate specific products of the enzymatic reaction (i.e., phosphopeptides) and release the nonspecific peptides to the solution. This strategy is simple, efficient, and successfully applied in the detection of phosphoproteins in real samples.

Facile synthesis of 4-mercaptophenylboronic acid functionalized gold nanoparticles for selective enrichment of glycopeptides

In the work, 4-mercaptophenylboronic acid (4-MPBA)-functionalized gold nanoparticles were synthesized via a facile approach. At first, gold nanoparticles (about 50 nm) were prepared by a simple and convenient hydrothermal method based on a polyol process. Then, gold nanoparticles were modified with 4-MPBA by the well-known reaction of Au with the thiol groups. The MPBA-functionalized gold nanoparticles were characterized by Fourier transform infrared spectra and UV/Vis adsorption spectra. Due to the fact that the boronic acid group on the surface of 4-MPBA-modified gold particles can form tight yet reversible covalent bonds with glycopeptides containing cis-1,2-diols groups, the MPBA-modified gold nanoparticles were successfully applied to selective enrichment of glycopeptides. Isolation and enrichment of glycopeptides in a standard protein (asialofetuin and horseradish peroxidase) digestion and a complex sample were performed using MPBA-modified gold nanoparticles, followed by matrix-assisted laser desorption/ionization quadruple ion trap time-of-flight (MALDI-QIT-TOF) mass spectrometric analysis. The experimental results demonstrated that MPBA-modified gold nanoparticles synthesized by the facile approach have the powerful potential for selective enrichment of glycopeptides, and can be an alternative tool in glycoproteomics.

Microfluidics with MALDI analysis for proteomics--a review

Various microfluidic devices have been developed for proteomic analyses and many of these have been designed specifically for mass spectrometry detection. In this review, we present an overview of chip fabrication, microfluidic components, and the interfacing of these devices to matrix-assisted laser desorption ionization (MALDI) mass spectrometry. These devices can be directly coupled to the mass spectrometer for on-line analysis in real-time, or samples can be analyzed on-chip or deposited onto targets for off-line readout. Several approaches for combining microfluidic devices with analytical functions such as sample cleanup, digestion, and separations with MALDI mass spectrometry are discussed.