Chip-based nanovials for tryptic digest and capillary electrophoresis

Evaporation from microreservoirs

As a result of very large surface area to volume ratios, evaporation is of significant importance when dealing with lab-on-a-chip devices that possess open air/liquid interfaces. For devices utilizing a reservoir as a fluid delivery method to a microfluidic network, excessive evaporation can quickly lead to reservoir dry out and overall device failure. Predicting the rates of evaporation from these reservoirs is difficult because the position of the air/liquid interface changes with time as the volume of liquid in the reservoir decreases. Here we present a two-step method to accurately predict the rates of evaporation of such an interface over time. First, a simple method is proposed to determine the shape of an air/liquid meniscus in a reservoir given a specific liquid volume. Second, computational fluid dynamics simulations are used to calculate the instantaneous rate of evaporation for that meniscus shape. It is shown that the rate of evaporation is strongly dependent on the overall geometry of the system, enhanced in expanding reservoirs while suppressed in contracting reservoirs, where the geometry can be easily controlled with simple experimental methods. Using no adjustable parameters, the model accurately predicts the position of the inner moving contact line as a function of time following meniscus rupture in poly(dimethylsiloxane) reservoirs, and predicts the overall time for the persistence of liquid in those reservoirs to within 0.5 minutes. The methods in this study can be used to design holding reservoirs for lab-on-a-chip devices that involve no external control of evaporation, such that evaporation rates can be adjusted as necessary by modification of the reservoir geometry.

Integrating accelerated tryptic digestion into proteomics workflows

An accelerated protein digestion procedure is described that features a microscale trypsin cartridge operated under aqueous-organic conditions. High sequence coverage digestions obtained in seconds with small amounts of enzyme are possible with the approach, which also supports online integration of digestion with reversed-phase protein separation. The construction and operation of effective digestor cartridges for rapid sample processing are described. For workflows involving chromatographic protein separation an easily assembled fluidic system is presented, which inserts the digestion step after column-based separation. Successful integration requires dynamic effluent titration immediately prior to transmission through the digestor. This is achieved through the co-ordination of the column gradient system with an inverse gradient system to produce steady pH and organic solvent levels. System assembly and operation sufficient for achieving digestion and identification of subnanogram levels of protein are described.

Managing evaporation for more robust microscale assays. Part 1. Volume loss in high throughput assays

Evaporation is a well known issue when handling small liquid volumes. Here we present a review of microscale assays prone to evaporation and methods to make them more robust. Applications for these assays span from combinatorial chemistry to cell-biology where the stability of concentrations and osmolarity can be critical. A dimensionless evaporation number Ev is presented and used to characterize volume loss in short term and long term microscale assays. Ev can be used both as a design tool and as an analysis parameter. The advantageous use of evaporation in some applications is also discussed.

Porous silicon protein microarray technology and ultra-/superhydrophobic states for improved bioanalytical readout

One attractive method for monitoring biomolecular interactions in a highly parallel fashion is the use of microarrays. Protein microarray technology is an emerging and promising tool for protein analysis, which ultimately may have a large impact in clinical diagnostics, drug discovery studies and basic protein research. This chapter is based upon several original papers presenting our effort in the development of new protein microarray chip technology. The work describes a novel 3D surface/platform for protein characterization based on porous silicon. The simple adjustment of pore morphology and geometry offers a convenient way to control wetting behavior of the microarray substrates. In this chapter, an interesting insight into the surface role in bioassays performance is made. The up-scaled fabrication of the novel porous chips is demonstrated and stability of the developed supports as well as the fluorescent bioassay reproducibility and data quality issues are addressed. We also describe the efforts made by our group to link protein microarrays to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), suggesting porous silicon as a convenient platform for fast on-surface protein digestion protocols linked to MS-readout. The fabrication of ultra- and superhydrophobic states on porous silicon is also described and the utilization of these water-repellent properties for a new microscaled approach to superhydrophobic MALDI-TOF MS target anchor chip is covered.

Microfabrication of screen-printed nanoliter vials with embedded surface-modified electrodes

A self-contained ion-selective sensing system within a nanoliter-volume vial has been developed by integrating screen printing, laser ablation, and molecular imprinting techniques. Screen printing and laser ablation are used in tandem to fabricate nanoliter-volume vials with carbon and Ag/AgCl ring electrodes embedded in the sidewalls. Using multisweep cyclic voltammetry, the surface of the carbon electrode can be modified with a polypyrrole film. By polymerizing pyrrole in the presence of nitrate, pores complementary to the nitrate anion in size, shape, and charge distribution are formed in the resulting film. Electrochemical cells modified with this nitrate-imprinted polypyrrole film show a near-Nernstian response to nitrate, and excellent reproducibility. The integration of molecular recognition and electrochemical response in the nanoliter vials is demonstrated by the detection of as little as 0.36 ng nitrate in nanoliter-volume samples. The integration of tailored molecular recognition within nanoliter vials via established fabrication and imprinting protocols should result in a number of nanosensor devices with applications in BioMEMS and micro total analysis systems.

Functionalized magnetic micro- and nanoparticles: Optimization and application to μ-chip tryptic digestion

The preparation of an easily replaceable protease microreactor for micro-chip application is described. Magnetic particles coated with poly(N-isopropylacrylamide), polystyrene, poly(2-hydroxyethyl methacrylate-co-ethylene dimethacrylate), poly(glycidyl methacrylate), [(2-amino-ethyl)hydroxymethylen]biphosphonic acid, or alginic acid with immobilized trypsin were utilized for heterogeneous digestion. The properties were optimized, with the constraint of allowing immobilization in a microchannel by a magnetic field gradient. To obtain the highest digestion efficiency, sub-micrometer spheres were organized by an inhomogeneous external magnetic field perpendicularly to the direction of the channel. Kinetic parameters of the enzyme reactor immobilized in micro-chip capillary (micro-chip immobilized magnetic enzyme reactor (IMER)) were determined. The capability of the proteolytic reactor was demonstrated by five model (glyco)proteins ranging in molecular mass from 4.3 to 150 kDa. Digestion efficiency of proteins in various conformations was investigated using SDS-PAGE, HPCE, RP-HPLC, and MS. The compatibility of the micro-chip IMER system with total and limited proteolysis of high-molecular-weight (glyco)proteins was confirmed. It opens the route to automated, high-throughput proteomic micro-chip devices.

Less common applications of monoliths: I. Microscale protein mapping with proteolytic enzymes immobilized on monolithic supports

This review summarizes the recent contributions to the rapidly growing area of immobilized enzymes employing both silica and synthetic polymer-based monoliths as supports. Focus is mainly on immobilized proteolytic enzyme reactors designed for studies in proteomics. Porous monoliths emerged first as a new class of stationary phases for HPLC in the early 1990s. Soon thereafter, they were also used as supports for immobilization of proteins and preparation of both stationary phases for bioaffinity chromatography and enzymatic reactors. Organic polymer-based monoliths are typically prepared using a simple molding process carried out within the confines of a "mold" such as chromatographic column or capillary. Polymerization of a mixture comprising monomers, initiator, and porogenic solvent affords macroporous materials. In contrast, silica-based monoliths are first formed as a rigid rod from tetraalkoxysilane in the presence of PEG and subsequently encased with a plastic tube. Both types of monolith feature large through-pores that enable a rapid flow-through. Since all the solutions must flow through the monolith, the convection considerably accelerates mass transfer within the monolith. As a result, reactors including enzyme immobilized on monolithic support exhibit much higher activity compared to the reactions in solution.

High-speed biomarker identification utilizing porous silicon nanovial arrays and MALDI-TOF mass spectrometry

Speed and accuracy are crucial prerequisites in the application of proteomic methods to clinical medicine. We describe a microfluidic-based nanovial array for rapid proteolytic processing linked to MALDI-TOF MS. This microscale format consumes only minute amounts of sample, and it is compatible with rapid bioanalytical protocols and high-sensitivity readouts. Arrays of vials (300 microm in diameter and 25 microm deep), isotropically etched in silicon wafers were electrochemically porosified. Automated picoliter microdispensing was employed for precise fluid handling in the microarray format. Vials were prefilled with trypsin solution, which was allowed to dry. Porosified and nonporosified nanovials were compared for trypsin digestion and subsequent MS identification of three model proteins: lysozyme, alcohol dehydrogenase, and serum albumin at levels of 100 and 20 fmol. In an effort to assess the rapid digestion platform in a context of putative clinical applications, two prostate cancer biomarkers, prostate-specific antigen (PSA) and human glandular kallikrein 2 (hK2), were digested at levels of 100 fmol (PSA), 20 fmol (PSA) and 8 fmol (hK2). All biomarker digestions were completed in less than 30 s, with successful MS identification in the porous nanovial setting.

Capillary electrophoretic and mass spectrometric analysis of a polydisperse fluorosurfactant

A fluorosurfactant has been studied using capillary electrophoresis and mass spectrometry. The fluorosurfactant, FC134, can be used as a buffer additive in capillary electrophoresis in order to decrease wall adsorption of proteins and in micellar electrokinetic chromatography. However, it has been discovered that this fluorosurfactant is polydisperse, thus containing substances with different lengths and structures. In this work, the fluorosurfactant sample components were separated by capillary electrophoresis. An uncoated as well as a poly(vinyl alcohol)-coated capillary were used with running electrolytes containing methanol and acetic acid. Following the capillary electrophoretic separation, fractions were collected for further analysis by MALDI-MS. Non-fractionated samples were also analyzed both by MALDI-MS and by ESI-MS.

Dual-Function Microanalytical Device by In Situ Photolithographic Grafting of Porous Polymer Monolith: Integrating Solid-Phase Extraction and Enzymatic Digestion for Peptide Mass Mapping

Microfluidic devices with a dual function containing both a solid-phase extractor and an enzymatic microreactor have been prepared, and their operation has been demonstrated. The devices were fabricated from a 25-mm-long porous poly(butyl methacrylate-co-ethylene dimethacrylate) monolith prepared within a 50-microm-i.d. capillary. This capillary with a pulled 9-12-microm needle tip was used as a nanoelectrospray emitter coupling the device to a mass spectrometer. Photografting with irradiation through a mask was then used to selectively functionalize a 20-mm-long portion of the monolith, introducing reactive poly(2-vinyl-4,4-dimethylazlactone) chains to enable the subsequent attachment of trypsin, thereby creating an enzymatic microreactor with high proteolytic activity. The other 5 mm of unmodified hydrophobic monolith served as micro solid-phase extractor (microSPE). The dual-function devices were used in two different flow directions; concentration of myoglobin that was absorbed from its dilute solution, followed by elution and digestion or digestion, followed by concentration. Operations in both directions afforded equal sequence coverage. Different volumes of myoglobin solution ranging from 2 to 20 microL were loaded on the device. Very high sequence coverages of almost 80% were achieved for the highest loading. Despite the very short length of the extractor unit, the device operated in the digest-solid-phase extraction direction also enabled the separation of peaks that mostly contained undigested protein and peptides.

Mass spectrometric study of the effects of hydrophobic surface chemistry and morphology on the digestion of surface-bound proteins

Our previous work has demonstrated that reversed-phase chromatographic micro-beads can be used to capture proteins from complex biological matrices and the surface-bound proteins can be enzymatically digested for protein identification by mass spectrometry (MS). Here we examine the peptides generated from digestion of proteins bound to various types of micro-bead surfaces in order to determine the effects of surface chemistry and surface morphology on the digestion process. Detailed examinations of site cleavages and sequence coverage are carried out for a tryptic digestion of cytochrome c adsorbed on reversed-phase polystyrene divinylbenzene (Poros R2 beads) versus C(18) bonded-phase silica beads. It is shown that although the surface does not completely hinder the digestion of cleavage sites of the protein, the digestion products are clearly different than those obtained from a solution digest. Specifically, a partial digestion results from surface digestion, resulting in a greater number of missed cleavages than a comparable solution digest. Subsequent comparisons of peptide mass maps generated from the digestion of various proteins on surfaces with altering chemistry (C(4), C(8), C(18), and R2 beads), or with different surface morphology, were performed. The results reveal that surface chemistry plays only a minor role in affecting the peptide mass maps, and surface morphology had no noticeable effects on the resulting peptide mass maps. It is also shown that the mass spectrometric detection method used to analyze the digested peptides can significantly influence the information content on cleavage sites and the extent of sequence coverage. The use of a combination of MALDI, LC/off-line MALDI, and LC/ESI MS is demonstrated to be crucial in revealing subtle changes in the peptide mass maps.

Membrane-based nanoscale proteolytic reactor enabling protein digestion, peptide separation, and protein identification using mass spectrometry

A miniaturized trypsin membrane reactor housed inside a commonly used capillary fitting is developed and demonstrated for enabling rapid and sensitive protein identification by on-line proteolytic digestion and analysis of protein digests using nano-ESI-MS and MALDI-MS. The design and assembly of the capillary fitting-based trypsin membrane reactor are straightforward and highly robust, without the need for expensive fabrication technology and procedures. The resultant protein digests can also be further concentrated and resolved using capillary reversed-phase liquid chromatography or transient capillary isotachophoresis/zone electrophoresis prior to the mass spectrometric analysis in an integrated platform. By comparing these results with the results obtained from our previous studies using plastic microfluidics (Gao et al., Anal. Chem. 2001, 73, 2648-2655), significant reduction in dead volume and sample consumption can be achieved using this newly developed tryptic digestion station. This nanoscale reaction system enables rapid proteolytic digestion in seconds instead of hours for a protein concentration of less than 10(-8) M, consumes very little sample (< or = 5 fmol), and offers capillary interfaces with various separation and mass spectrometry techniques. The ultrafast enzymatic turnover for attaining complete peptide coverage in protein identification is contributed by the highly porous structure of the membrane media, providing excessive trypsin loading while eliminating the constraints of diffusion-limited reaction kinetics.

Microcolumn capture and digestion of proteins combined with mass spectrometry for protein identification

A procedure has been developed for protein identification using mass spectrometry (MS) that incorporates sample cleanup, preconcentration, and protein digestion in a single-stage system. The procedure involves the adsorption of a protein, or protein mixture, from solution onto a hydrophobic resin that is contained within a microcolumn. Sample loading is accomplished by flowing the protein solution through the microcolumn, where the protein adsorbs to the hydrophobic surface. The protein is digested while still bound to the hydrophobic surface by flowing a buffered trypsin solution through the column bed. The peptide fragments are subsequently eluted for detection by MALDI or ESI-MS. The procedure is demonstrated using dilute protein samples containing high concentrations of salt, urea, and modest amount of sodium dodecyl sulfate relative to protein. Peptide fragments are also detected by MS from a 500 nM bacteriorhodopsin solution digested in a microcolumn. In this case, a combined cyanogen bromide/trypsin digestion was performed in-column. The procedure is applied to the MALDI-MS/MS identification of proteins present in an individual fraction collected by ion exchange HPLC separation of E. coli total cell extract. An additional application is illustrated in the analysis of a human plasma fraction. A total of 14 proteins, which were present in the sample at sub-micromolar concentrations, were identified from ESI-MS/MS. The microcolumn digestion procedure represents the next step toward a system for fully automated protein analysis through capture and digestion of the adsorbed protein on hydrophobic surfaces.

Enzymatic microreactor-on-a-chip: protein mapping using trypsin immobilized on porous polymer monoliths molded in channels of microfluidic devices

Enzymatic microreactors have been prepared in capillaries and on microfluidic chips by immobilizing trypsin on porous polymer monoliths consisting of 2-vinyl-4,4-dimethylazlactone, ethylene dimethacrylate, and acrylamide or 2-hydroxyethyl methacrylate. The azlactone functionalities react readily with amine and thiol groups of the enzyme to form stable covalent bonds. The optimized porous properties of the monoliths lead to very low back pressures enabling the use of simple mechanical pumping to carry out both the immobilization of the enzyme from its solution and the subsequent analyses of substrate solutions. The Michealis-Menten kinetic characteristics of the reactors were probed using a low molecular weight substrate: N-alpha-benzoyl-L-arginine ethyl ester. The effects of immobilization variables such as the concentration of trypsin in solution and percentage of azlactone functionalities in the monolith, as well as the effect of reaction time on the enzymatic activity, and of process variables such as substrate flow velocity and residence time in the reactor, were studied in detail. The proteolytic activity of the enzymatic microreactor on chip was demonstrated at different flow rates with the cleavage of fluorescently labeled casein used as a substrate. The excellent performance of the monolithic microreactor was also demonstrated with the digestion of myoglobin at the fast flow rate of 0.5 microL/min, which affords a residence time of only 11.7 s. The digest was then characterized using MALDI-TOF MS, and 102 out of 153 possible peptide fragments were identified giving a sequence coverage of 67%.

Bioanalysis in microfluidic devices

Microfabricated bioanalytical devices (also referred to as laboratory-on-a-chip or micro-TAS) offer highly efficient platforms for simultaneous analysis of a large number of biologically important molecules, possessing great potential for genome, proteome and metabolome studies. Development and implementation of microfluidic-based bioanalytical tools involves both established and evolving technologies, including microlithography, micromachining, micro-electromechanical systems technology and nanotechnology. This article provides an overview of the latest developments in the key device subject areas and the basic interdisciplinary technologies. Important aspects of DNA and protein analysis, interfacing issues and system integration are all thoroughly discussed, along with applications for this novel "synergized" technology in high-throughput separations of biologically important molecules. This review also gives a better understanding of how to utilize these technologies as well as to provide appropriate technical solutions to problems perceived as being more fundamental.

Nanotiterplates for combinatorial chemistry

Miniaturization has grown to be a driving force in modern chemical and biochemical laboratories. Combinatorial explosion demands for new pathways for the synthesis and screening of new substances which can act as leads in drug discovery. Highly parallelized automata that can handle the smallest amounts of substances are needed. However, the development is not always straightforward since new problems also arise in miniaturization, e.g. increasing importance of surface properties of utilized devices and evaporation of liquids. This paper reports on recent developments on the field of miniaturized reaction vessels called nanotiterplates. A survey on fabrication technologies as well as applications of nanotiterplates is given. Special emphasis is given to results of the development of an automaton for miniaturized synthesis and screening. Besides the mere fabrication of nanotiterplates with integrated microsieve bottom membranes, examples of applications in chemical synthesis and bio-assays are given. Further topics are the characterization and specific adaption of surface properties and investigations on the evaporation of solvents and measures for prevention.

Recent advances in capillary electrophoresis of peptides

The article gives a comprehensive review on the recent developments in the applications of high-performance capillary electromigration methods, including zone electrophoresis, isotachophoresis, isoelectric focusing, affinity electrophoresis, electrokinetic chromatography and electrochromatography, to analysis, preparation and physicochemical characterization of peptides. The article presents new approaches to the theoretical description and experimental verification of electromigration behavior of peptides, and covers the methodological aspects of capillary electroseparations of peptides, such as strategy and rules for the rational selection of separation mode and experimental conditions, sample treatment, suppression of peptide adsorption to the inner capillary wall, new developments in individual separation modes and new designs of detection systems. Several types of applications of capillary electromigration methods to peptide analysis are presented: conventional qualitative and quantitative analysis for determination of purity, determination in biomatrices, monitoring of physical and chemical changes and enzymatic conversions, amino acid and sequence analysis and peptide mapping of proteins. Some examples of micropreparative peptide separations are given and capabilities of capillary electromigration techniques to provide important physicochemical characteristics of peptides are demonstrated.

Wall deactivation with fluorosurfactants for capillary electrophoretic analysis of biomolecules

This paper describes the use of fluorosurfactants as buffer additives for capillary electrophoretic separation of proteins and peptides. Due to fluorosurfactant bilayer formation at the capillary inner wall, the surface charge can be adjusted and even reversed. If the running buffer pH is kept at a level where the proteins have the same sign of charge as the wall, electrostatic repulsion will be obtained. The protein wall adsorption can therefore be reduced and the separation performance can be noticeably increased. The separation performance can also be further improved by including mixtures of different types of fluorosurfactants in the running buffer. The buffer system can accordingly be adapted for a certain separation problem. Mechanisms for the use of fluorosurfactants for wall deactivation in capillary electrophoretic protein separations is discussed in the present work and some examples of applications are also presented.

Proteomics on a chip: promising developments

The field of proteomics is expanding rapidly due to the completion of the human genome and the realization that genomic information is often insufficient to comprehend cellular mechanisms. This considerable expansion of proteomics towards high-throughput platforms is stressing its current technical capabilities. In recent years, technologies in microfluidic and array technologies have appeared for proteomics. These novel approaches might help solve current technical challenges in proteomics. This review presents a general survey of the recent development in microfluidic and array technologies from a proteomics perspective.

Liquid lid for biochemical reactions in chip-based nanovials

The present paper describes a new technique to suppress evaporation of solvent from very small volumes. Vials (15 nl) on a silicon microchip were filled with water, and covered with a thin, flowing film of a volatile liquid (e.g., octane). Water evaporation was greatly reduced. At 37 degrees C, no appreciable loss of water could be observed over a period of 90 min. At 95 degrees C, most of the water sample was left in the vial for more than 3 min. The applicability of the method is demonstrated by a tryptic digest, where the resulting peptide fragments were analyzed by capillary electrophoresis. In addition, a discussion of the possibilities and limitations of some alternative methods is included in the paper, as well as an outlook on future developments of the liquid lid concept.

Parallel reactions in open chip-based nanovials with continuous compensation for solvent evaporation

In an earlier report (Litborn, E., Emmer, A., Roeraade, J., Anal. Chim. Acta 1999, 401, 11-19, we described a technique for performing chemistry in chip-based vials. A major problem, solvent evaporation, was partially remedied by using a closed humidity chamber. In this paper we report an improved technique for performing parallel reactions in open, 15 nL volume, chip-based vials. The evaporation of solvent from the reaction fluid was continuously compensated by addition of solvent via an array of microcapillaries. The suitability of the method was demonstrated by performing eight separate peptide maps of myoglobin in parallel, using the three enzymes trypsin, alpha-chymotrypsin and endoproteinase Glu-C. The total amount of myoglobin utilized to perform the eight digests was less than 100 pmol. The corresponding amount of enzymes was ca. 0.1 pmol per reaction. In order to evaluate the operating limits of the technique, a study of the evaporation of solvents from a series of vials with proportionally smaller volumes operated at different temperatures was performed. The results showed that the concept for continuous compensation of solvent evaporation should be applicable to reaction volumes down to 30 pL.