Fluorescence-labeled peptide pI markers for capillary isoelectric focusing

Nineteen fluorescent pH standards or pI markers ranging pH 3.64-10.12 were developed for use in capillary isoelectric focusing using laser-induced fluorescence detection. Tetra- to tridecapeptides containing one cysteine residue were designed to focus sharply at their respective isoelectric points by including amino acids that contain charged side chains, the pKa values of which are close to the corresponding pI values. An iodoacetylated derivative of tetramethylrhodamine was coupled to the thiol group of cysteine to yield fluorescent pI markers. The pI values of the labeled peptides were precisely determined after isoelectric focusing on polyacrylamide gel slabs by direct measurement of the pH of the focused bands. The markers were subjected to capillary isoelectric focusing for 10-15 min in coated capillaries under conditions of low electroosmosis and were detected by means of a scanning laser-induced fluorescence detector down to a level of subpicomolar range. The markers permitted the calibration of a wide-range pH gradient formed in a capillary by fluorescence detection for the first time and should facilitate the development of highly sensitive analytical methods based on a combination of capillary isoelectric focusing and laser-induced fluorescence detection.     

Microfluidic high-resolution free-flow isoelectric focusing

A microfluidic free-flow isoelectric focusing glass chip for separation of proteins is described. Free-flow isoelectric focusing is demonstrated with a set of fluorescent standards covering a wide range of isoelectric points from pH 3 to 10 as well as the protein HSA. With respect to an earlier developed device, an improved microfluidic FFE chip was developed. The improvements included the usage of multiple sheath flows and the introduction of preseparated ampholytes. Preseparated ampholytes are commonly used in large-scale conventional free-flow isoelectric focusing instruments but have not been used in micromachined devices yet. Furthermore, the channel depth was further decreased. These adaptations led to a higher separation resolution and peak capacity, which were not achieved with previously published free-flow isoelectric focusing chips. An almost linear pH gradient ranging from pH 2.5 to 11.5 between 1.2 and 2 mm wide was generated. Seven isoelectric focusing markers were successfully and clearly separated within a residence time of 2.5 s and an electrical field of 20 V mm-1. Experiments with pI markers proved that the device is fully capable of separating analytes with a minimum difference in isoelectric point of Delta(pI) = 0.4. Furthermore, the results indicate that even a better resolution can be achieved. The theoretical minimum difference in isoelectric point is Delta(pI) = 0.23 resulting in a peak capacity of 29 peaks within 1.8 mm. This is an 8-fold increase in peak capacity to previously published results. The focusing of pI markers led to an increase in concentration by factor 20 and higher. Further improvement in terms of resolution seems possible, for which we envisage that the influence of electroosmotic flow has to be further reduced. The performance of the microfluidic free-flow isoelectric focusing device will enable new applications, as this device might be used in clinical analysis where often low sample volumes are available and fast separation times are essential.     

High-resolution capillary isoelectric focusing of complex protein mixtures from lysates of microorganisms

High-resolution capillary isoelectric focusing separations of complex protein mixtures have been obtained for cellular lysates of Saccharomyces cerevisiae, Eschericia coli, and Deinococcus radiodurans. High quality separations are shown to be achievable for total protein concentrations of < 0.1 mg/mL. The separation reproducibility was examined, and the influence of the capillary inner wall coating on resolution investigated using fusedsilica capillaries coated with various hydrophilic polymers including hydroxypropyl cellulose, poly(vinyl alcohol), and linear polyacrylamide. Proteins having an isoelectric point (pI) difference of 0.004 are shown to be separated using a linear carrier ampholyte (linear pH gradient between two electrodes) of 3-10. Approximately 45 discrete peaks in the pI range of 5-7 were obtained for S. cerevisiae, approximately 80 peaks in the pI range of 4.5-8.5 for E. coli, and approximately 210 peaks in the pI range of 3-8.8 for D. radiodurans.     

Capillary isoelectric focusing of individual mitochondria

Mitochondria are highly heterogeneous organelles that likely have unique isoelectric points (pI), which are related to their surface compositions and could be exploited in their purification and isolation. Previous methods to determine pI of mitochondria report an average pI. This article is the first report of the determination of the isoelectric points of individual mitochondria by capillary isoelectric focusing (cIEF). In this method, mitochondria labeled with the mitochondrial-specific probe 10-N-nonyl acridine orange (NAO) are injected into a fused-silica capillary in a solution of carrier ampholytes at physiological pH and osmolarity, where they are focused then chemically mobilized and detected by laser-induced fluorescence (LIF). Fluorescein-derived pI markers are used as internal standards to assign a pI value to each individually detected mitochondrial event, and a mitochondrial pI distribution is determined. This method provides reproducible distributions of individual mitochondrial pI, accurate determination of the pI of individual mitochondria by the use of internal standards, and resolution of 0.03 pH units between individual mitochondria. This method could also be applied to investigate or design separations of organelle subtypes (e.g., subsarcolemmal and interfibrillar skeletal muscle mitochondria) and to determine the pIs of other biological or nonbiological particles.     

On-chip isoelectric focusing using photopolymerized immobilized pH gradients

We present the first successful adaptation of immobilized pH gradients (IPGs) to the microscale (muIPGs) using a new method for generating precisely defined polymer gradients on-chip. Gradients of monomer were established via diffusion along 6 mm flow-restricted channel segments. Precise control over boundary conditions and the resulting gradient is achieved by continuous flow of stock solutions through side channels flanking the gradient segment. Once the desired gradient is established, it is immobilized via photopolymerization. Precise gradient formation was verified with spatial and temporal detection of a fluorescent dye added to one of the flanking streams. Rapid (<20 min) isoelectric focusing of several fluorescent pI markers and proteins is demonstrated across pH 3.8-7.0 muIPGs using both denaturing and nondenaturing conditions, without the addition of carrier ampholytes. The muIPG format yields improved stability and comparable resolution to prominent on-chip IEF techniques. In addition to rapid, high-resolution separations, the reported muIPG format is amenable to multiplexed and multidimensional analysis via custom gradients as well as integration with other on-chip separation methods.     

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.     

Separation of polypeptides by isoelectric point focusing in electrospray-friendly solution using a multiple-junction capillary fractionator

We introduce an online multiple-junction capillary isoelectric focusing fractionator (OMJ-CIEF) for separation of biological molecules in solution by pI. In OMJ-CIEF, the separation capillary is divided into seven equal sections joined with each other via tubular Nafion membrane insertions. Each junction is communicated with its own external electrolytic buffer which is used both to supply electrical contact and for solvent exchange. The performance of the fractionator was explored using protein and peptide samples covering broad pI range. Separation was achieved in ionic and ampholytic buffers, including ammonium formate, ammonium hydroxide, histidine, and arginine. By maintaining electric potential across upstream segments of the capillary after the focusing stage, selective release of downstream analyte fractions could be achieved. The selective release mode circumvents the problem of peak broadening during mobilization and enables convenient comprehensive sampling for orthogonal separation methods. Using single-component ampholyte buffers with well-defined pI cutoff values, controlled separation of protein mixture into basic and acidic fractions was demonstrated. The device is cheap and easy to fabricate in-house, simple in operation, and straightforward in interfacing to hyphened analytical platforms. OMJ-CIEF has a potential of becoming a practical add-on unit in a wide range of bioanalytical setups, in particular as a first-dimension separation in mass spectrometry based proteomics or as a preparative tool for analyte purification, fractionation, and preconcentration.     

Isoelectric point determination of norovirus virus-like particles by capillary isoelectric focusing with whole column imaging detection

A capillary isoelectric focusing-whole column imaging detection (CIEF-WCID) method was used to determine the isoelectric point (pI) of norovirus virus-like particles (VLPs). The VLPs were produced from noroviruses that represented the two genogroups, genogroup I (Funabashi, Seto, and Norwalk) and genogroup II (Hawaii, Kashiwa, and Narita). Using the imaged CIEF-WCID detection technique, separation was accomplished using a short (4-5 cm) internally coated capillary (100-microm diameter) and a whole-column optical absorption imaging detector operated at 280 nm. CIEF-WCID experiments showed the similarity of the pI values of VLPs from genogroups I and II, with pI values of 5.9, 5.9, 6.0, and 6.0 for Funabashi, Norwalk, Seto, and Hawaii. The two other VLPs displayed pI values of 5.5 (Kashiwa) and 6.9 (Narita). The VLP peaks were shown to be reproducibility resolved. CIEF-WCID shows great promise for norovirus detection in public health, clinical, and food safety applications, as CIEF-WCID overcomes several limitations of the currently used genetic and immunological methods.     

Capillary isoelectric focusing and fluorometric detection of proteins and microorganisms dynamically modified by poly(ethylene glycol) pyrenebutanoate

The nonionogenic pyrene-based tenside, poly(ethylene glycol) pyrenebutanoate, was prepared and applied in capillary isoelectric focusing with fluorometric detection. This dye was used here as a buffer additive in capillary isoelectric focusing for a dynamic modification of the sample of proteins and microorganisms. The values of the isoelectric points of the labeled bioanalytes were calculated with use of the fluorescent pI markers and were found comparable with pI of the native compounds. The mixed cultures of proteins and microorganisms, Escherichia coli CCM 3954, Staphylococcus epidermidis CCM 4418, Proteus vulgaris, Enterococcus faecalis CCM 4224, and Stenotrophomonas maltophilia, the strains of the yeast cells, Candida albicans CCM 8180, Candida krusei, Candida parapsilosis, Candida glabrata, Candida tropicalis, and Saccharomyces cerevisiae were reproducibly focused and separated by the suggested technique. Using UV excitation for the on-column fluorometric detection, the minimum detectable amount was down to 10 cells injected on the separation capillary.     

Isoelectric focusing in a microfluidically defined electrophoresis channel

A new form of microchip isoelectric focusing that allows efficient coupling with pretreatment processes is reported. The sample is conveyed in a carrier ampholyte solution to the separation channel that is connected at both ends by two V-shaped lead channels, which supply electrode solutions to the connection point and complete the electrical connection to off-chip electrodes. The relatively high electric conductivity of the electrode solutions compared with that of the pH gradient enables focusing with a 2% loss of applied voltage at the electrodes using the lead channels. A glass microchip was constructed specifically for this configuration. The channel wall was coated with polydimethylacrylamide, and the IEF chip was operated in a chip holder equipped with on-chip connector valves. A plug of fluorescence-labeled peptide p I markers with p I values ranging from 3.64 to 9.56 with carrier ampholyte solution (pH 3-10) was introduced into the separation channel. When the plug reached the channel segment (24 mm in length) between the connection points with the electrolyte lead channels, isoelectric focusing was started after filling the lead channels with electrolyte solutions. The peptide markers were observed using scanning fluorescence detection. The entire range of the pH gradient was established in the segment after approximately 2 min. Isoelectric focusing of three consecutively injected sample plugs containing different p I markers was demonstrated.     

Multistage isoelectric focusing in a polymeric microfluidic chip

This paper reports a protocol that improves the resolving power of isoelectric focusing (IEF) in a polymeric microfluidic chip. This method couples several stages of IEF in series by first focusing proteins in a straight channel using broad-range ampholytes and then refocusing segments of the first channel into secondary channels that branch from the first one at T-junctions. Experiments demonstrate that several fluorescent proteins that had focused within a segment of the straight channel in the first stage were refocused at significantly higher resolution due to the shallower pH gradient and higher electrical field gradient. Two variants of green fluorescent protein from the second-stage IEF fractionation were further separated in a third stage. Three stages of IEF were completed in less than 25 min at electric field strengths ranging from 50 to 214 V/cm.     

Microscale isoelectric fractionation using photopolymerized membranes

In this work, we introduce microscale isoelectric fractionation (μIF) for isolation and enrichment of molecular species at any desired location in a microfluidic chip. Narrow pH-specific polyacrylamide membranes are photopatterned in situ for customizable device fabrication; multiple membranes of precise pH are easily incorporated throughout existing channel layouts. Samples are electrophoretically driven across the membranes such that charged species, for example, proteins and peptides, are rapidly discretized into fractions based on their isoelectric points (pI) without the use of carrier ampholytes. This format makes fractions easy to compartmentalize and access for integrated preparative or analytical operations on-chip. We present and discuss the key design considerations and trade-offs associated with proper system operation and optimal run conditions. Efficient and reproducible fractionation of model fluorescent pI markers and proteins is achieved using single membrane fractionators at pH 6.5 and 5.3 from both buffer and Escherichia coli cell lysate sample conditions. Effective fractionation is also shown using a serial 3-membrane fractionator tailored for isolating analytes-of-interest from high abundance components of serum. We further demonstrate that proteins focused in pH specific bins can be rapidly and efficiently transferred to another location in the same chip without unwanted dilution or dispersive effects. μIF provides a rapid and versatile option for integrated sample prep or multidimensional analysis, and addresses the glaring proteomic need to isolate trace analytes from high-abundance species in minute volumes of complex samples.     

High-efficiency capillary isoelectric focusing of peptides

Several approaches are presently being developed for global proteome characterization that are based upon the analysis of polypeptide mixtures resulting from digestion of (often complex) mixtures of proteins. Improved methods for peptide analysis are needed that provide for sample concentration, higher resolution separations, and direct compatibility with mass spectrometry. In this work, methods for the high-efficiency capillary isoelectric focusing (CIEF) separation of peptides have been developed that provide for simultaneous sample concentration and separation according to peptide isoelectric point. Under typical nondenaturing CIEF conditions, peptides are concentrated approximately 500-fold, and peptides present at < 1 ng/ microL were detectable using conventional UV detection. CIEF separations of peptides provided much faster measurements of isoelectric points compared with conventional isoelectric focusing in gels. Very small differences in peptide isoelectric points (deltapI approximately 0.01) could be resolved, High-efficiency CIEF separations for complex peptide mixtures from tryptic digestion of yeast cytosol fractions were obtained and showed significant improvement over those obtained using capillary zone electrophoresis and packed capillary reversed-phase liquid chromatography.     

High-resolution capillary isoelectric focusing-electrospray ionization mass spectrometry for hemoglobin variants analysis

On-line capillary isoelectric focusing (CIEF)-electrospray ionization mass spectrometry (ESIMS) as a two-dimensional separation system is employed for high-resolution analysis of hemoglobin variants A, C, S, and F. The effects of moving ionic boundary inside the CIEF capillary and MS scan rate on the separation resolution and mass detection of hemoglobin variants are investigated. The formation of a moving ionic boundary due to the replacement of background electrolyte counterions with sheath liquid counterions can be minimized by combining cathodic mobilization with a gravity-induced hydrodynamic flow. Hemoglobin variants F and A, with a pI difference of 0.05 pH unit, are almost baseline resolved and identified in CIEF-ESIMS. The concentration detection limit for each hemoglobin variant is in the range of 10(-)(8) M, comparable to that obtained in two-dimensional gel electrophoresis using silver staining. Initial preconcentration during the focusing step and the use of single-ion monitoring scan mode are responsible for improving detection limits.     

Dynamic isoelectric focusing for proteomics

Dynamic isoelectric focusing is a new technique that is related to capillary isoelectric focusing but uses additional high-voltage power supplies to provide control over the shape of the electric field within the capillary. Manipulation of the electric field changes the pH gradient, enabling both the location and width of the focused protein bands to be controlled. The proteins can be migrated to a designated sampling point while remaining focused, where they can be collected for further analysis. This ability to collect and isolate the protein bands while maintaining a high peak capacity demonstrates that dynamic isoelectric focusing has great potential as a first dimension in a multidimensional separation system. Dynamic isoelectric focusing can achieve a peak capacity of over 1000, as shown by both mass spectrometry analysis and direct imaging.     

Flow-through microvial facilitating interface of capillary isoelectric focusing and electrospray ionization mass spectrometry

A capillary electrophoresis mass spectrometry (CE-MS) interface utilizing a flow-through microvial is used to ensure the electric continuity and supply the catholyte and mobilizer solutions during the capillary isoelectric focusing (cIEF) and mobilization process. The flow-through microvial provides a stable chemical environment and helps to improve the ionization efficiency without significantly diluting the analyte. The CE-MS interface facilitates the transfer of the mobilized cIEF effluent to the site of electrospray ionization, and the gaseous ions can be detected directly by a mass spectrometer. It also allows for complete focusing and mobilization processes to be performed automatically in programmed sequences with commercial CE systems. Two different strategies, using either a part of the capillary or the flow-through microvial of the CE-MS interface as the catholyte reservoir for bare fused silica capillaries or neutral coated capillaries, respectively, were developed for automated cIEF-electrospray ionization (ESI)-MS. Reasonable separation efficiency was achieved using proper concentration of carrier ampholytes and suitable strategies of electroosmotic/electrophoretic mobilization.     

Selective focusing of catecholamines and weakly acidic compounds by capillary electrophoresis using a dynamic pH junction

A systematic study of selective analyte focusing in a multisection electrolyte system by capillary electrophoresis (CE) is presented. It was found that a dynamic pH junction between sample and background electrolyte zones can be used to focus zwitterionic catecholamines and weakly acidic compounds without the use of special ampholytes. Differences in pH and concentration of complexing agents, such as borate, in the sample and background electrolyte zones were determined to cause focusing through changes in the local velocity of the analyte in two different segments of the capillary. Velocity-difference induced focusing (V-DIF) of analytes using a dynamic pH junction allowed the injection of large sample volumes and significantly improved the concentration sensitivity of CE. Under optimized conditions, the limit of detection for epinephrine was determined to be about 4 x 10(-8) M (the original sample) with conventional UV absorbance detection. Moreover, separation efficiencies greater than a million theoretical plates can be achieved by focusing such large sample volumes into narrow zones. Multisection electrolyte systems, which lead to the formation of a dynamic pH junction, can be tuned toward improving the concentration sensitivity of specific analytes if their chemical properties are known.     

Nanoliter-volume selective sampling of peptides based on isoelectric points for MALDI-MS

A simple way to selectively isolate peptides based on their isoelectric points (pI) for MALDI mass spectral analysis is described. An applied voltage was used to electromigrate peptides into a capillary. The capillary was modified with a zwitterionic surfactant, 1,2-dilauroyl-sn-phosphatidylcholine (DLPC), to suppress the electroosmotic flow (EOF) during injection. Hence, either the cationic or the anionic peptides were introduced, depending on the voltage polarity. By controlling the pH, selective loading of peptides was performed to isolate trace components from a mixture. The injected sample plugs were subsequently spotted in nanoliter volumes for MALDI-MS analysis. No significant sample losses resulting from selective sampling were detected. Low attomole-level detection of peptides (adrenocorticotropic hormone fragment 18-39, pI 4.25) was achieved from a mixture containing other peptides (angiotensin I, pI 6.92, and bradykinin, pI 12.00) at 100 000-fold higher concentrations.     

Analytical- and preparative-scale isoelectric focusing separation of enantiomers

Isoelectric focusing has been used to achieve the analytical- and preparative-scale separation of the enantiomers of amphoteric analytes. By considering the simultaneous multiple equilibria involved in the chiral recognition process, a model has been developed to describe the magnitude of the ΔpI value that develops between the enantiomers in the presence of a noncharged chiral resolving agent, such as a noncharged cyclodextrin. Theoretical analysis of the model indicates that three kinds of IEF enantiomer separations are possible: aniono-selective and cationo-selective, when only the identically charged forms of the enantiomers bind selectively to the resolving agent, and duo-selective, when the differently charged forms of the enantiomers bind selectively to the resolving agent. The model predicts that the ΔpI vs cyclodextrin concentration curves approach limiting ΔpI values which can be as large as 0.1, even when the binding constants of the enantiomers differ only by 10%. The parameters of the model can be readily determined by free solution capillary electrophoretic or pressure-mediated capillary electrophoretic experiments. The validity of the proposed model has been tested with hydroxypropyl β-cyclodextrin as resolving agent and dansyl phenylalanine as probe. Capillary IEF enantiomer separations have been achieved using both ampholytes and binary propionic acid-serine buffers (Bier's buffers). Preparative-scale IEF enantiomer separations with production rates as high as 1.3 mg/h have been achieved in an Octopus continuous free-flow electrophoretic system.