Instrumentation for medium-throughput two-dimensional capillary electrophoresis with laser-induced fluorescence detection

In two-dimensional capillary electrophoresis, a sample undergoes separation in the first dimension capillary by sieving electrophoresis. Fractions are periodically transferred across an interface into a second dimension capillary, where components are further resolved by micellar electrokinetic capillary electrophoresis. Previous instruments employed one pair of capillaries to analyze a single sample. We now report a multiplexed system that allows separation of five samples in parallel. Samples are injected into five first-dimension capillaries, fractions are transferred across an interface to 5 second-dimension capillaries, and analyte is detected by laser-induced fluorescence in a five-capillary sheath-flow cuvette. The instrument produces detection limits of 940 +/- 350 yoctomoles for 3-(2-furoyl)quinoline-2-carboxaldehyde labeled trypsin inhibitor in one-dimensional separation; detection limits degrade by a factor of 3.8 for two-dimensional separations. Two-dimensional capillary electrophoresis expression fingerprints were obtained from homogenates prepared from a lung cancer (A549) cell line, on the basis of capillary sieving electrophoresis (CSE) and micellar electrophoresis capillary chromatography (MECC). An average of 131 spots is resolved with signal-to-noise greater than 10. A Gaussian surface was fit to a set of 20 spots in each electropherogram. The mean spot width, expressed as standard deviation of the Gaussian function, was 2.3 +/- 0.7 transfers in the CSE dimension and 0.46 +/- 0.25 s in the MECC dimension. The standard deviation in spot position was 1.8 +/- 1.2 transfers in the CSE dimension and 0.88 +/- 0.55 s in the MECC dimension. Spot capacity was 300.     

Two-dimensional electrochromatography/capillary electrophoresis on a microchip

A two-dimensional separation system on a microfabricated device was demonstrated using open-channel electrochromatography as the first dimension and capillary electrophoresis as the second dimension. The first dimension was operated under isocratic conditions, and the effluent from the first dimension was repetitively injected into the second dimension every few seconds. A 25-cm separation channel with spiral geometry for open-channel electrochromatography was chemically modified with octadecylsilane and coupled to a 1.2-cm straight separation channel for capillary electrophoresis. Fluorescently labeled products from tryptic digests of beta-casein were analyzed in 13 min with this system.     

A capillary array gel electrophoresis system using multiple laser focusing for DNA sequencing

A very simple and highly sensitive capillary array gel electrophoresis system is constructed to analyze DNA fragments. On-column detection of DNA migration in a large number of gel-filled capillaries is carried out using side-entry laser irradiation and with a CCD camera, although it has been considered impossible because the irradiation laser is scattered strongly at the surfaces of the first few capillaries. By optimizing optical conditions, the laser beam can be focused repeatedly to irradiate all the capillaries held on a plate by working each capillary as a cylindrical convex lens. DNA sequencing samples migrating in 24 capillaries can simultaneously be analyzed with the system.     

Fabrication of a poly(dimethylsiloxane)-based electrochemiluminescence detection cell for capillary electrophoresis

An easy but effective technique is described here for quick fabrication of low-cost electrochemiluminescence detection cells for capillary electrophoresis. The technique is based on molding of poly(dimethylsiloxane) (PDMS) with a capillary column inserted into a pipet tip. Two access holes are left in the PDMS slab; they provide neat accommodations for the separation capillary and the working electrode made with the same type of tip. Since the access holes are well-aligned, the electrode and the capillary are automatically aligned; thus, end-column detection is easily obtained. Fabrication of the detection cell is straightforward; no micromechanical operation is included. Also the principle for the procedure makes it possible to efficiently batch production detection cells with good reproducibility. Because of the end-column scheme, the cell can be adopted for electrophoresis with electrochemical detection as well.     

Heart-cutting two-dimensional capillary electrophoresis for the on-line purification and separation of derivatized amino acids

Heart-cutting two-dimensional (2D) capillary electrophoresis (CE) in a single capillary was used for analysis of derivatized amino acids. A mixture of 12 amino acids derivatized with UV-active benzyl 4-(3-(2-chloroethyl)-3-nitrosoureido)butylcarbamate label served as a model of a moderately complex sample due to the presence of numerous derivatization byproducts. The first step of the heart-cutting 2D approach was sample cleanup by capillary zone electrophoresis (CZE) in borate electrolyte. Then, only a selected portion of the first-dimension separation was transferred into the second dimension of the separation by a specific voltage and pressure program. Finally, the zone of derivatized amino acids was separated by micellar electrokinetic chromatography in a borate-sodium dodecyl sulfate system. The whole 2D process can be performed in a conventional CE analyzer without any interface for connection of the two separation modes. Intraday repeatability of the total migration time was 2%. In general, the heart-cutting 2D-CE methodology in a single capillary can be adapted for any CE mode regardless of the direction and velocity of electroosmotic flow and position of the fraction of interest in the first dimension (i.e., first, last, or intermediate fraction).     

CE-microreactor-CE-MS/MS for protein analysis

We present a proof-of-principle for a fully automated bottom-up approach to protein characterization. Proteins are first separated by capillary electrophoresis. A pepsin microreactor is incorporated into the distal end of this capillary. Peptides formed in the reactor are transferred to a second capillary, where they are separated by capillary electrophoresis and characterized by mass spectrometry. While peptides generated from one digestion are being separated in the second capillary, the next protein fraction undergoes digestion in the microreactor. The migration time in the first dimension capillary is characteristic of the protein while migration time in the second dimension is characteristic of the peptide. Spot capacity for the two-dimensional separation is 590. A MS/MS analysis of a mixture of cytochrome c and myoglobin generated Mascot MOWSE scores of 107 for cytochrome c and 58 for myoglobin. The sequence coverages were 48% and 22%, respectively.     

Two-dimensional electrophoretic separation of proteins using poly(methyl methacrylate) microchips

The work presented herein describes highly efficient, two-dimensional (2D) electrophoretic separations of proteins in a PMMA-based microchip. Sodium dodecyl sulfate microcapillary gel electrophoresis (SDS micro-CGE) and micellar electrokinetic chromatography (MEKC) were used as the separation modes for the first and second dimension of the electrophoresis, respectively. The microchip was prepared by hot embossing into PMMA from a brass mold master fabricated via high-precision micromilling. The microchip incorporated a 30-mm SDS micro-CGE and a 10-mm MEKC dimension length. Electrokinetic injection and separation were used with field strengths of up to 400 V/cm. Alexa Fluor 633 conjugated proteins, ranging in size from 38 to 110 kDa, were detected using laser-induced fluorescence with excitation/emission at 633/652 nm. Average plate numbers (N) of 4.8 x 10(4) and 1.2 x 10(4) were obtained in the SDS micro-CGE and MEKC separation dimensions, respectively, for the investigated proteins corresponding to plate heights (H) of 0.62 and 0.87 microm. Effluents from the first dimension (SDS micro-CGE) were repetitively transferred into the second dimension every 0.5 s of run time in the first dimension with the electrophoresis run time in the MEKC dimension being 10 s. The 2D separation was performed on the investigated proteins in approximately 12 min and provided a peak capacity of approximately 1000.     

Comparison of two-dimensional fractionation techniques for shotgun proteomics

Two-dimensional (2D) fractionation is a commonly used tool to increase dynamic range and proteome coverage for bottom-up, shotgun proteomics. However, there are few reports comparing the relative separation efficiencies of 2D methodologies using low-microgram sample quantities. In order to systematically evaluate 2D separation techniques, we fractionated microgram quantities of E. coli protein extract by seven different methods. The first dimension of separation was performed with either reversed-phase high-pressure liquid chromatography (RP-HPLC), gel electrophoresis (SDS-PAGE), or strong cation exchange (SCX-HPLC). The second dimension consisted of a standard reversed-phase capillary HPLC coupled to an electrospray ionization quadrupole time-of-flight mass spectrometer for tandem mass spectrometric analysis. The overall performance and relative fractionation efficiencies of each technique were assessed by comparing the total number of proteins identified by each method. The protein-level RP-HPLC and the high-pH RP-HPLC peptide-level separations performed the best, identifying 281 and 266 proteins, respectively. The online pH variance SCX and the SDS-PAGE returned modest performances with 178 and 139 proteins identified, respectively. The offline SCX had the worst performance with 81 proteins identified. We also examined various chromatographic factors that contribute to separation efficiency, including resolving power, orthogonality, and sample loss.     

On-line hyphenation of capillary isoelectric focusing and capillary gel electrophoresis by a dialysis interface

An on-line two-dimensional (2D) capillary electrophoresis (CE) system consisting of capillary isoelectric focusing (CIEF) and capillary gel electrophoresis (CGE) was introduced. To validate this 2D system, a dialysis interface was developed by mounting a hollow fiber on a methacrylate resin plate to hyphenate the two CE modes. The two dimensions of capillary shared a cathode fixated into a reservoir in the methacrylate plate; thus, with three electrodes and only one high-voltage source, a 2D CE framework was successfully established. A practical 2D CIEF-CGE experiment was carried out to deal with a target protein, hemoglobin (Hb). After the Hb variants with different isoelectric points (pIs) were focused in various bands in the first-dimension capillary, they were chemically mobilized one after another and fed to the second-dimension capillary for further separation in polyacrylamide gel. During this procedure, a single CIEF band was separated into several peaks due to different molecular weights. The resulting electrophoregram is quite different from that of either CIEF or CGE; therefore, more information about the studied Hb sample can be obtained.     

Automated instrumentation for comprehensive isotachophoresis-capillary zone electrophoresis

An automated comprehensive isotachophoresis-capillary zone electrophoresis (ITP-CZE) system is described. The sample is focused in the first capillary by ITP and injected repeatedly into the second smaller diameter capillary for more rapid CZE separation. Since only small portions of the concentrated zones are sequentially injected for CZE separation, overloading was not observed. Moreover, the sensitivity is enhanced because all of the concentrated zones are analyzed and the results are summed. A single detector (only for the CZE dimension) is required, and accurate timing for CZE injection is not necessary. The system was evaluated using a mixture of angiotensins. The effect of addition of leading electrolyte at the junction of the ITP and CZE capillaries before each CZE run on comprehensive ITP-CZE peak area was studied, and leading electrolyte volumes between 7 and 11 microL led to the best sensitivity. Under optimized conditions, a detection limit of approximately 5 nM could be achieved by injecting 10 microL of angiotensin solution.     

Separation of DNA restriction fragments by capillary electrophoresis using coated fused silica capillaries.

The abilities of several different capillary electrophoresis techniques to separate DNA restriction fragments up to 23,000 bp were investigated. Methods employing electroosmotic flow in an untreated silica capillary were found to provide, at best, only partial resolution of the 23 fragments in a 1-kbp DNA ladder. By coating the inner walls of a silica capillary with poly(acrylamide) and filling these capillaries with buffers containing methylcellulose as a sleving medium, all fragments in the 1-kbp DNA ladder were separated. In addition, this technique facilitated the separation of the very large fragments in a lambda DNA-HindIII digest. Optimum resolution was obtained at low separation potentials using buffers containing at least 0.5% methylcellulose. The performance of this technique, i.e., resolution and quantitation, make capillary electrophoresis a powerful complement to slab gel electrophoresis and may make it a preferred alternative to both agarose gel electrophoresis and HPLC for applications such as the confirmation of plasmid integrity.     

Programmed nebulizing gas pressure for efficient and stable capillary electrophoresis-mass spectrometry analysis of anionic compounds in positive separation mode

Here we have developed a method for the analysis of anionic compounds by capillary electrophoresis coupled to electrospray ionization-mass spectrometry (CE-ESI-MS). The strategy proposed is based on the application of programmed nebulizing gas pressure (PNP), which is applied during the different steps of analysis: sample injection, electrophoretic separation, and detection by the mass spectrometer. The proposed procedure prevents the frequent drops in current observed in the analysis of anions and allows high separation efficiency by capillary electrophoresis to be maintained because it is not necessary to employ pressured-assisted electrophoresis. Additionally, for the first time we describe the use of 100 μm capillaries in capillary electrophoresis-mass spectrometry, allowing the loading of larger samples and hence greater sensitivity, with no loss of the efficiency achieved with the 50 μm capillaries usually used.     

Integration of isoelectric focusing with parallel sodium dodecyl sulfate gel electrophoresis for multidimensional protein separations in a plastic microfluidic [correction of microfludic] network

An integrated protein concentration/separation system, combining non-native isoelectric focusing (IEF) with sodium dodecyl sulfate (SDS) gel electrophoresis on a polymer microfluidic chip, is reported. The system provides significant analyte concentration and extremely high resolving power for separated protein mixtures. The ability to introduce and isolate multiple separation media in a plastic microfluidic network is one of two key requirements for achieving multidimensional protein separations. The second requirement lies in the quantitative transfer of focused proteins from the first to second separation dimensions without significant loss in the resolution acquired from the first dimension. Rather than sequentially sampling protein analytes eluted from IEF, focused proteins are electrokinetically transferred into an array of orthogonal microchannels and further resolved by SDS gel electrophoresis in a parallel and high-throughput format. Resolved protein analytes are monitored using noncovalent, environment-sensitive, fluorescent probes such as Sypro Red. In comparison with covalently labeling proteins, the use of Sypro staining during electrophoretic separations not only presents a generic detection approach for the analysis of complex protein mixtures such as cell lysates but also avoids additional introduction of protein microheterogeneity as the result of labeling reaction. A comprehensive 2-D protein separation is completed in less than 10 min with an overall peak capacity of approximately 1700 using a chip with planar dimensions of as small as 2 cm x 3 cm. Significant enhancement in the peak capacity can be realized by simply raising the density of microchannels in the array, thereby increasing the number of IEF fractions further analyzed in the size-based separation dimension.     

An automated on-line multidimensional HPLC system for protein and peptide mapping with integrated sample preparation

A comprehensive on-line two-dimensional 2D-HPLC system with integrated sample preparation was developed for the analysis of proteins and peptides with a molecular weight below 20 kDa. The system setup provided fast separations and high resolving power and is considered to be a complementary technique to 2D gel electrophoresis in proteomics. The on-line system reproducibly resolved approximately 1000 peaks within the total analysis time of 96 min and avoided sample losses by off-line sample handling. The low-molecular-weight target analytes were separated from the matrix using novel silica-based restricted access materials (RAM) with ion exchange functionalities. The size-selective sample fractionation step was followed by anion or cation exchange chromatography as the first dimension. The separation mechanism in the subsequent second dimension employed hydrophobic interactions using short reversed-phase (RP) columns. A new column-switching technique, including four parallel reversed-phase columns, was employed in the second dimension for on-line fractionation and separation. Gradient elution and UV detection of two columns were performed simultaneously while loading the third and regenerating the fourth column. The total integrated workstation was operated in an unattended mode. Selected peaks were collected and analyzed off-line by MALDI-TOF mass spectrometry. The system was applied to protein mapping of biological samples of human hemofiltrate as well as of cell lysates originating from a human fetal fibroblast cell line, demonstrating it to be a viable alternative to 2D gel electrophoresis for mapping peptides and small proteins.     

Sweeping with electrokinetic injection and analyte focusing by micelle collapse in two-dimensional separation via integration of micellar electrokinetic chromatography with capillary zone electrophoresis

A novel integrated concentration/separation approach involving online combination of sweeping with electrokinetic injection and analyte focusing by micelle collapse (AFMC) with heart-cutting two-dimensional (2D) capillary electrophoresis (CE) in a single capillary was developed for analysis of Herba Leonuri and mouse blood samples. First, a new sweeping with an electrokinetic injection preconcentration method was developed to inject a large volume sample solution and significantly enhance detection sensitivity. Then, the preconcentration scheme was integrated to the 2D-CE to provide significant analyte concentration and extremely high resolving power. The sample was preconcentrated by sweeping with electrokinetic injection and separated in first dimension micellar electrokinetic chromatography (MEKC). Then, only a desirable fraction of the first dimension separation was transferred into the second dimension of the capillary by pressure and further analyzed by capillary zone electrophoresis (CZE) acting as the second dimension. As the key to successful integration of MEKC and CZE, an AFMC step was integrated between the two dimensions to release analytes from the micelle interior to a liquid zone and to overcome the sample zone diffusion caused by mobilization pressure. The injected sample plug lengths for flavonoids under 15 kV for 60 min were experimentally estimated as 546 cm. The dual concentration methods resulted in the increased detection factors of 6000-fold relative to the traditional pressure injection method. The relative standard deviation (RSD) values of peak height, peak area, and migration time were 2.7-4.5%, 1.9-4.3%, and 4.7-6.8% (n = 10), respectively. The limits of detection (S/N = 3) were in the range of 7.3-36.4 ng/L, and the theoretical plate numbers (N) were in the range of 1.7-4.3 × 10(4) plates/m. This method has been successfully applied to determine flavonoids in Herba Leonuri and postdosing mouse blood samples. The pharmacokinetic study also demonstrated that the proposed concentration/separation method was convenient and sensitive and would become an attractively alternative method for online sample concentration and separation in complex samples.     

High-speed free-flow electrophoresis on chip

A microfluidic device has been developed for continuous separation in free-flow electrophoresis (FFE) mode. A mixture of two fluorescent reagents is separated into two component streams in 75 ms using a sample flow rate of 2 nL/s. The residence time of sample in the whole separation compartment is 2 s. The separation bed volume is 0.2 microL. The chip has also been used for free-flow electrophoresis of fluorescein-5-isothiocyanate-labeled amino acids in both aqueous and binary media. The short residence time and small sample flow rate make the FFE chip feasible for on-line monitoring on production lines and other chemical or biochemical processes. The in-house-made chip was composed of a plain glass substrate of 1.5-mm thickness and a PDMS layer of 0.3-mm thickness with micromachined channels. The channel design presented in this paper is versatile. With the same kind of PDMS substrates, chips for various purposes can be made depending on the locations of the reservoirs, which are cut out on the PDMS substrate. The results presented verify the scaling laws and allow prediction of FFE performances comparable to what is now state of the art on capillary electrophoresis chips.     

Considerations on orthogonality duality in comprehensive two-dimensional gas chromatography

The term "orthogonal" in comprehensive two-dimensional gas chromatography (GC × GC) has a double sided meaning as it stands for a separation resulting from the combination of two independent retention mechanisms (Giddings, J. C. J. High Resolut. Chromatogr. 1987, 10, 319) but also for a 2D separation where the components are evenly distributed over the entire 2D space. It is shown in the present study that a nonorthogonal GC × GC system associating a polar stationary phase in the first dimension (poly(ethylene glycol)) to a nonpolar one in the second dimension (poly(dimethyl siloxane)) leads to a structured chromatogram, a high peak capacity, and a great 2D space occupation. This idea is demonstrated through the characterization of oxygenated compounds in a coal-derived middle distillate. Results show a clear separation between oxygenated species and hydrocarbons which are classified into linear alkanes, cyclic alkanes, and aromatics. A breakthrough configuration combining a polar poly(ethylene glycol) first dimension and a trifluoropropyl methyl stationary phase in the second dimension enabled a unique identification and quantification of linear, cyclic, and aromatic alcohols. This configuration which could be considered as nonorthogonal still involves two different retention mechanisms: polarity and boiling point in the first dimension and electronic interactions in the second dimension. It is selective toward electronegative poles of alcohols and phenols. The contributions of these two configurations compared to a conventional orthogonal system as well as their roles for oxygenated compounds speciation are highlighted. This contribution is measured through three 2D space occupation factors. It appears through these two examples that orthogonality is intimately linked to analyte properties, and a general concept of dimensionality must be considered.     

Specific base recognition of oligodeoxynucleotides by capillary affinity gel electrophoresis using polyacrylamide-poly(9-vinyladenine) conjugated gel.

Poly(9-vinyladenine) was synthesized and utilized as an affinity macroligand entrapped within the gel matrix. Base-specific separation of oligodeoxynucleotides was achieved with high resolution and high speed by electrophoresis, using capillaries filled with conjugated polyacrylamide-poly(9-vinyladenine) gel. Oligothymidylic acids were selectively separated from the mixture of oligothymidylic and oligodeoxyadenylic acids by utilizing a specific hydrogen bonding between poly(9-vinyladenine) and oligothymidylic acids. Migration time and resolution of oligodeoxynucleotides were influenced by several parameters, such as the size of poly(9-vinyladenine), capillary temperature, and concentrations of poly(9-vinyladenine) and urea. Some guidelines are presented, based on the theoretical formulation of the effect of these parameters, in order to find optimum electrophoretic conditions. Analytical capillary affinity gel electrophoresis was developed for the selective and sensitive base recognition of oligodeoxynucleotides with efficiencies as high as several 10(6) plates/m by using a urea-gel capillary with poly(9-vinyladenine) and temperature-programming.     

Capillary electrophoresis as a second dimension to isoelectric focusing for peptide separation

Capillary zone electrophoresis and carrier ampholytes based capillary electrophoresis have been used as a second separation step to Off-Gel isoelectric focusing for the analysis of complex peptide mixtures. A tryptic digest of four proteins (bovine serum albumin, beta-lactoglobulin, horse myoglobin, cytochrome c) has been chosen as a peptide test mixture. After assessment of different modes of capillary electrophoresis as a second dimension to Off-Gel isoelectric focusing, the optimized two-dimensional platforms provide a degree of orthogonality comparable to state-of-the-art multidimensional liquid chromatography systems as well as a practical peak capacity above 700.     

Rapid Prototyping of Microfluidic Systems in Poly(dimethylsiloxane)

This paper describes a procedure that makes it possible to design and fabricate (including sealing) microfluidic systems in an elastomeric material [Formula: see text] poly(dimethylsiloxane) (PDMS) [Formula: see text] in less than 24 h. A network of microfluidic channels (with width >20 μm) is designed in a CAD program. This design is converted into a transparency by a high-resolution printer; this transparency is used as a mask in photolithography to create a master in positive relief photoresist. PDMS cast against the master yields a polymeric replica containing a network of channels. The surface of this replica, and that of a flat slab of PDMS, are oxidized in an oxygen plasma. These oxidized surfaces seal tightly and irreversibly when brought into conformal contact. Oxidized PDMS also seals irreversibly to other materials used in microfluidic systems, such as glass, silicon, silicon oxide, and oxidized polystyrene; a number of substrates for devices are, therefore, practical options. Oxidation of the PDMS has the additional advantage that it yields channels whose walls are negatively charged when in contact with neutral and basic aqueous solutions; these channels support electroosmotic pumping and can be filled easily with liquids with high surface energies (especially water). The performance of microfluidic systems prepared using this rapid prototyping technique has been evaluated by fabricating a miniaturized capillary electrophoresis system. Amino acids, charge ladders of positively and negatively charged proteins, and DNA fragments were separated in aqueous solutions with this system with resolution comparable to that obtained using fused silica capillaries.