Linear Polyacrylamide-coated Capillary Research Articles

Integrated MICROFASP Method with CZE-Based Fractionation Technique and NanoRPLC-ESI-MS/MS for a Comprehensive Proteomics Analysis of a Submicrogram Sample.

We report a loss-less two-dimensional (2D) separation platform that integrated capillary zone electrophoresis (CZE) fractionation and nanoRPLC-ESI-MS/MS for a comprehensive proteomics analysis of a submicrogram sample. Protein digest was injected into the linear polyacrylamide-coated capillary, followed by CZE separation. The schemes for collecting the fractions were carefully optimized to maximize the protein coverage. The peptide fractions were directly eluted into the autosampler insert vials, followed by the nanoRPLC-ESI-MS/MS analysis without lyophilization and redissolution, thus dramatically minimizing sample loss and potential contamination. The integrated platform generated 30,845 unique peptides and 5231 protein groups from 500 ng of a HeLa protein digest within 11.5 h (90 min CZE fractionation plus 10 h LC-MS analysis). Finally, the developed platform was used to analyze the protein digest prepared by the MICROFASP method with 1 μg of cell lysate as the starting material. Three thousand seven hundred ninety-six (N = 2, RSD = 4.95%) protein groups and 20,577 (N = 2, RSD = 7.89%) peptides were identified from only 200 ng of the resulted tryptic digest within 5.5 h. The results indicated that the combination of the MICROFASP method and the developed CZE/nanoRPLC-MS/MS 2D separation platform enabled comprehensive proteome profiling of a submicrogram biological sample. Data are available via ProteomeXchange with the identifier PXD052735.

Top-Down Proteomics by Capillary Zone Electrophoresis-Tandem Mass Spectrometry for Large-Scale Characterization of Proteoforms in Complex Samples.

Capillary zone electrophoresis (CZE) is a fundamentally simple and highly efficient separation technique based on differences in electrophoretic mobilities of analytes. CZE-mass spectrometry (MS) has become an important analytical tool in top-down proteomics which aims to delineate proteoforms in cells comprehensively, because of the improvement of capillary coatings, sample stacking methods, and CE-MS interfaces. Here, we present a CZE-MS/MS-based top-down proteomics procedure for the characterization of a standard protein mixture and an Escherichia coli (E. coli) cell lysate using linear polyacrylamide-coated capillaries, a dynamic pH junction sample stacking method, a commercialized electro-kinetically pumped sheath flow CE-MS interface and an Orbitrap mass spectrometer. CZE-MS/MS can identify hundreds of proteoforms routinely from the E. coli sample with a 1% proteoform-level false discovery rate (FDR).

Monitoring the crosstalk between methylation and phosphorylation on histone peptides with host-assisted capillary electrophoresis.

Post-translational modifications (PTMs) greatly increase protein diversity and regulate their functions by changing the structures, properties, and molecular interactions of proteins. In peptide regions with high density of PTMs, PTMs can influence modification on residues in proximity or even at distal positions, adding another layer of regulation. Methods that can monitor the activities of PTM enzymes on peptides carrying multiple modifications are valuable tools for better understanding of PTM crosstalk. Herein, we developed a host-assisted capillary electrophoresis (CE) method to separate histone peptides with methylation and phosphorylation and applied it to monitor the crosstalk between serine phosphorylation and lysine methylation when they were added by Aurora B kinase and G9a lysine methyltransferase, respectively. A synthetic receptor molecule, 4-hexasulfonatocalix[6]arene (CX6), was included in the CE buffer to improve the resolution of the corresponding substrates and products. A linear polyacrylamide-coated capillary was employed to effectively reduce wall adsorption of the cationic histone peptides. The peptide substrates were labeled with fluorescein to enhance their detectability during CE separation. Our method successfully revealed that the activity of G9a methyltransferase was completely inhibited by the adjacent phosphorylation, while 25% reduction in the activity of Aurora B kinase was observed with the presence of dimethylation on the nearby residue. The PTM crosstalk was examined not only using a pure peptide substrate, but also in a competitive reaction environment, in which the modified and unmodified peptides were mixed and the enzyme actions on both peptides were monitored simultaneously. Our work demonstrates that host-assisted CE is an effective method for study of PTM crosstalk, which could offer the advantages of fast separation, high resolution, and low sample consumption. Graphical abstract.

Bottom-up proteome analysis of E. coli using capillary zone electrophoresis-tandem mass spectrometry with an electrokinetic sheath-flow electrospray interface

The Escherichia coli proteome was digested with trypsin and fractionated using SPE on a C18 SPE column. Seven fractions were collected and analyzed by CZE-ESI-MS/MS. The separation was performed in a 60-cm-long linear polyacrylamide-coated capillary with a 0.1% v/v formic acid separation buffer. An electrokinetic sheath-flow electrospray interface was used to couple the separation capillary with an Orbitrap-Velos operating in higher-energy collisional dissociation mode. Each CZE-ESI-MS/MS run lasted 50 min and total MS time was 350 min. A total of 23706 peptide spectra matches, 4902 peptide IDs, and 871 protein group IDs were generated using MASCOT with false discovery rate less than 1% on the peptide level. The total mass spectrometer analysis time was less than 6 h, the sample identification rate (145 proteins/h) was more than two times higher than previous studies of the E. coli proteome, and the amount of sample consumed (<1 μg) was roughly fourfold less than previous studies. These results demonstrate that CZE is a useful tool for the bottom-up analysis of prokaryote proteomes.

High‐resolution computer simulations of EKC

The electrophoresis simulation software, GENTRANS, has been modified to include the interaction of analytes with an electrolyte additive to allow the simulation of liquid-phase EKC separations. The modifications account for interaction of weak and strong acid and base analytes with a single weak or strong acid or base background electrolyte additive and can be used to simulate a range of EKC separations with both charged and neutral additives. Simulations of separations of alkylphenyl ketones under real experimental conditions were performed using mobility and interaction constant data obtained from the literature and agreed well with experimental separations. Migration times in fused-silica capillaries and linear polyacrylamide-coated capillaries were within 7% of the experimental values, while peak widths were always narrower than the experimental values, but were still within 50% of those obtained by experiment. Simulations of sweeping were also performed; although migration time agreement was not as good as for simple EKC separations, peak widths were in good agreement, being within 1-50% of the experimental values. All simulations for comparison with experimental data were performed under real experimental conditions using a 47 cm capillary and a voltage of 20 kV and represent the first quantitative attempt at simulating EKC separations with and without sweeping.

Long‐term precision in capillary isoelectric focusing for protein analysis

In order to improve precision in protein analysis, a new rinsing procedure with 3M hydrochloric acid was investigated for linear polyacrylamide-coated capillaries used in isoelectric focusing. After each run the capillaries were rinsed with hydrochloric acid for 5 min, followed by water for 20 min (Deltap = 1030 mbar each). Myoglobin, beta-lactoglobulin, and ovalbumin were used as model proteins; the pH gradient was provided by Pharmalyte (pH 3-10). The resulting method was already successful in avoiding capillary blockages, even for long-series protein measurements. Further improvements in precision have been obtained by avoiding a complete standstill of liquid within the capillary when the separation system was idle. Pressure (Deltap = 300 mbar or more) and high voltage (30 kV) were therefore also applied during storage within a measurement series. The reproducibility of migration time and peak area are further improved with RSD% less than 10% in a long-term measurement (n = 86).

Reproducible protein analysis by CE using linear polyacrylamide‐coated capillaries and hydrochloric acid rinsing

Hydrochloric acid was investigated as a rinsing reagent to remove adsorbed proteins from linear polyacrylamide-coated capillaries for electrophoresis. Three model proteins were used, namely cytochrome c as a basic protein, beta-lactoglobulin as an acidic protein, and beta-casein as a more easily denaturing protein. In order to regenerate capillary surfaces, they have been rinsed for 5 min with 2 M hydrochloric acid, 5 min with water, and then 30 min with buffer after every tenth run. It was found important to perform this regeneration procedure on time. The obtained results show good repeatability of the apparent EOF mobility with percentage RSDs below 3% (n = 60) in various cases. These good results were mainly confirmed in long-term series with more than 200 runs each. Only very high concentrations (175 microM) of beta-lactoglobulin and beta-casein at pH 3.5 gave RSD% values above 5%. For these conditions, the further test of 85% m/m phosphoric acid as rinsing reagent showed a good repeatability of the apparent EOF mobilities as well.

Protein adsorption in fused-silica and polyacrylamide-coated capillaries

The model proteins cytochrome c, myoglobin, ovalbumin, and beta-lactoglobulin were investigated with regard to their adsorption properties on capillaries for electrophoresis. The model compounds were selected to cover a wide range of properties. Cytochrome c is a basic protein (isoelectric point (pI): 9.6; M(r): 11.7 kDa), beta-lactoglobulin is rather acidic (pI: 5.4, M(r): 18.4 kDa), myoglobin was chosen as a neutral reference protein (pI: 6.8-7.4, M(r): 17.8 kDa), and ovalbumin (pI: 5.1, M(r): 45.0 kDa) was selected as a relatively larger analyte. First, the pH dependence of adsorption was investigated for the bare fused silica. A clear correlation to the respective pIs was noted. For myoglobin and ovalbumin, none or negligible adsorption was found above the pI, whereas strong adsorption was noted just below this parameter. Cytochrome c and beta-lactoglobulin already showed distinct adsorption above their pIs. However, none of the proteins showed any significant adsorption more than one pH unit above the pIs. For linear polyacrylamide-coated capillaries, a decreased but not a complete lack of adsorption was observed. Here, pH-dependent adsorption was noted as well. Regeneration of the capillaries by rinsing with buffers containing 200 mM SDS was also investigated. This method was completely successful for myoglobin, but that too for only freshly-adsorbed protein. After a storage time of 24 h and due to the aging of the adsorbate, a sufficient regeneration was no longer possible.

Enantioseparation of α-Quaternary Amino Amides by Capillary Electrophoresis with Human Serum Albumin

Enantiomers of nine α-quaternary phenyl amino amides were synthesized and separated for the first time by capillary electrophoresis (CE). Human serum albumin (HSA) was selected as a useful anionic chiral selector by the aid of electrostatic interaction between the anionic selector and the cationic solutes. Partial-filling technique and linear polyacrylamide-coated capillaries were employed so that high concentration of HSA could be used to achieve high resolution without the loss of detection sensitivity. HSA concentration and buffer pH were shown critical and have to be optimized. It was found the hindrance effect of substituent played important role in enantioseparation.

Structural requirements for conserved Arg 52 residue for interaction of the human immunodeficiency virus type 1 trans-activation responsive element with trans-activator of transcription protein (49–57) : Capillary electrophoresis mobility shift assay

A sensitive capillary electrophoresis mobility shift assay (CEMSA) for qualitative study of the interaction between the trans-activation response element (TAR) and the trans-activator of transcription protein (Tat) has been presented. The human immunodeficiency virus type 1 (HIV-1) Tat promotes elongation of viral mRNAs binding to the TAR. It has been suggested that a single, conserved arginine residue (presumably Arg 52) within the arginine-rich region (ARR) of Tat plays the major role for the Tat–TAR recognition. To study structural requirements of the Arg 52 position, Tat(49–57)–NH 2 analogues substituted with nonencoded amino acids at the Arg 52 position have been synthesized and their interaction with TAR has been studied by CEMSA. Using a linear polyacrylamide-coated capillary and a sieving polymer containing separation buffer, well separated and shaped peaks of free and bound TAR RNA were obtained. In the presence of Tat1 peptide bearing the native sequence of Tat(49–57) a significant shift of migration time of TAR from 18.66 min (RSD=1.4%) to 20.12 min (RSD=2.4%) was observed. We have found that almost every substitution within the guanidino group of the Arg 52 [L-Arg 52→Cit, →Orn, →Arg(NO 2), →Arg(Me 2)] strongly disrupted or abolished the TAR–Tat peptide interaction. Enantiomeric substitution, L-Arg 52→D-Arg was the only one which notably promoted TAR–Tat peptide interaction. The results demonstrate that the specific net of hydrogen bonds created by the guanidinio group of conserved Arg 52 plays a crucial role for TAR–Tat HIV-1 recognition. The newly developed procedure describes for the first time use of CE to monitor RNA–peptide complex formation. The methodology presented should be generally applicable to study RNA–peptide (protein) interaction.

Separation of basic drug enantiomers by capillary zone electrophoresis using glucuronyl glucosyl beta-cyclodextrin as a chiral selector.

Separations of basic drug enantiomers have been investigated using glucuronyl glucosyl beta-cyclodextrin (GUG beta-CD) as a chiral selector in the background electrolyte by capillary zone electrophoresis. The effects of GUG beta-CD concentration and running buffer pH on the migration times and resolution of 16 basic drug enantiomers were precisely examined using a linear polyacrylamide-coated capillary. High resolution of 16 basic drug enantiomers was generally attained with a running buffer pH 2.5 or 3.5 containing 10 mM GUG beta-CD. Next, we compared the chiral resolution abilities of GUG beta-CD with those of beta-CD and maltosyl beta-CD (G2 beta-CD). GUG beta-CD showed higher resolution for basic drug enantiomers tested than beta-CD and G2 beta-CD. This could be due to that hydrogen bonding or ionic interactions of uncharged and charged glucuronyl glucosyl groups of GUG beta-CD with an analyte could stabilize the inclusion complex.

Separation of basic drug enantiomers by capillary electrophoresis using ovoglycoprotein as a chiral selector: Comparison of chiral resolution ability of ovoglycoprotein and completely deglycosylated ovoglycoprotein

Separations of basic drug enantiomers by capillary electrophoresis (CE) using ovoglycoprotein (OGCHI) as a chiral selector are described. The effects of running buffer pH and 2-propanol content on the migration times and resolution of basic drug enantiomers were examined using a linear polyacrylamide-coated capillary. High resolution of basic drug enantiomers was attained using a mixture of 50 mM sodium phosphate buffer (pH 4.5–6.0) and 2-propanol (5–30%) including 50 νM OGCHI. It was found that ionic and hydrophobic interactions could work for the recognition of basic drug enantiomers. Further, we compared the chiral resolution ability of OGCHI with that of completely deglycosylated OGCHI (cd-OGCHI) using them as chiral selectors in CE. OGCHI showed higher resolution for basic drug enantiomers tested than cd-OGCHI. The results suggest that the chiral recognition site(s) for OGCHI exists on the protein domain of OGCHI.

Separation of basic drug enantiomers by capillary zone electrophoresis using glucuronyl glucosyl β-cyclodextrin as a chiral selector

Separations of basic drug enantiomers have been investigated using glucuronyl glucosyl beta-cyclodextrin (GUG beta-CD) as a chiral selector in the background electrolyte by capillary zone electrophoresis. The effects of GUG beta-CD concentration and running buffer pH on the migration times and resolution of 16 basic drug enantiomers were precisely examined using a linear polyacrylamide-coated capillary. High resolution of 16 basic drug enantiomers was generally attained with a running buffer pH 2.5 or 3.5 containing 10 mM GUG beta-CD. Next, we compared the chiral resolution abilities of GUG beta-CD with those of beta-CD and maltosyl beta-CD (G2 beta-CD). GUG beta-CD showed higher resolution for basic drug enantiomers tested than beta-CD and G2 beta-CD. This could be due to that hydrogen bonding or ionic interactions of uncharged and charged glucuronyl glucosyl groups of GUG beta-CD with an analyte could stabilize the inclusion complex.

Characterization of M proteins as a series of peaks by capillary zone electrophoresis with a linear polyacrylamide-coated capillary.

Human serum proteins including myeloma (M) proteins were analyzed by capillary zone electrophoresis (CZE) using a linear polyacrylamide-coated capillary at pH 7.4. Each of the M proteins, IgG-κ, IgA-κ, and IgA-λ, which were located on the β zone on the cellulose acetate electrophoresis (CAE), was resolved into a group of peaks with a unique profile in a wide area following the transferrin (TF) peak. While the IgG-κ showed a series of narrow peaks, IgA-κ and IgA-λ showed a wide peak with many successive spikes. On the other hand, the increased polyclonal IgA-κ and IgG-κ, which were located on the β zone on the CAE, showed only a broad peak around the TF peak. Another IgG-κ M protein, which was located on the γ zone on the CAE, did not appear on the CZE at pH 7.4, but did appear with several peaks by increasing the pH to 9.0. No peaks were observed in the area following the TF peak when healthy serum proteins including immunoglobulins (Igs) were analyzed at both pHs. The coexistence of albumin did not affect the detection of monoclonal and polyclonal Igs. These results demonstrate that the CZE system is capable of distinguishing IgG M proteins from IgA M proteins, and monoclonal Igs from polyclonal ones. Furthermore, it was found that the CZE is useful for discriminating between isoforms of IgG M proteins.

Electrophoretic studies of polygalacturonate oligomers and their interactions with metal ions.

Polygalacturonic acid, a linear homopolysaccharide, was investigated by capillary electrophoresis (CE) using linear polyacrylamide-coated capillaries and laser-induced fluorescence (LIF) detection. A successful separation of its fluorescently labeled oligomers was achieved through sieving in polyacrylamide entangled matrices. The reaction conditions for the derivatization of polygalacturonic acid were optimized. In studying the interactions between polygalacturonic acid and various metal ions, the end-label, free-solution electrophoretic (ELFSE) technique, developed earlier in our laboratory (Sudor, J., Novotny, M. V., Anal. Chem. 1995, 67, 4205-4209) was found preferable to the sieving method. ELFSE is fast and convenient in that no polymer solutions are needed for the separation. The investigation showed that for the moderately large oligomers, the strongest binding occurred with calcium and cadmium ions, while the smallest interaction was observed with magnesium ions.

Rapid identification of metallothionein isoforms in liver cytosol fraction by capillary zone electrophoresis using EDTA

Identification of metallothionein (MT) isoforms on capillary zone electrophoresis (CZE) analysis was studied using a linear polyacrylamide-coated capillary at pH 7.4 and EDTA. The CZE system was able to separate standard (purified and commercially available) MT specimens into their isoforms within 10 min. The peaks of MT-1 and MT-2 isoforms disappeared on addition of EDTA to the specimen, and the disappearance was shown to be time-dependent and dose-dependent, although the reason why the peaks decreased is still unclear. A heat-treated cytosol fraction prepared from Zn-injected mouse liver showed many major and minor peaks on CZE analysis. Two major peaks were identified to be MT-1 and MT-2, respectively, by co-injection with the purified MT isoforms. When EDTA was added to the cytosol fraction, the two major peaks, MT-1 and MT-2, and three other minor peaks disappeared time-dependently. Therefore, each MT isoform in the cytosol fraction can be identified by the addition of EDTA, also the peaks are identified by the corresponding migration times of purified MTs. Unknown substances like MT sub-isoforms may also be detected, although this question warrants clarification. From these results, it was concluded that the addition of EDTA is useful for identification of MT isoforms in cytosol fractions on CZE analysis.

Capillary zone electrophoresis of albumin-depleted human serum using a linear polyacrylamide-coated capillary: separation of serum alpha-and beta-globulins into individual components.

The separation of human serum globulins into individual components was investigated by capillary zone electrophoresis (CZE) using a linear polyacrylamide-coated capillary at pH 7.4. Prior to CZE analysis of globulin components present in serum, it was found that it was necessary to remove albumin. Preparation of albumin-depleted human serum with a HiTrap Blue column allowed the detection of alpha- and beta-globulin components as a series of peaks. Almost all the peaks, both narrow and broad, observed in CZE analysis could be assigned to six globulin components (alpha1-acid-glycoprotein, alpha1 -antitrypsin, haptoglobin, alpha2-macroglobulin, Gc-globulin, and transferrin) by using the technique of antibody-based indirect detection. The CZE results, obtained from serum preparations from three healthy adults and six patients, showed that the CZE system might be capable of detecting qualitative differences among individuals with regard to individual globulin components.

Capillary zone electrophoresis of albumin-depleted human serum using a linear polyacrylamide-coated capillary: Separation of serum α-and β-globulins into individual components

Capillary zone electrophoresis of albumin-depleted human serum using a linear polyacrylamide-coated capillary: Separation of serum α-and β-globulins into individual components

Preparation of linear polyacrylamide-coated capillaries: Study of the polymerization process and its effect on capillary electrophoresis performance

The effect of different parameters controlling the characteristics of linear polyacrylamide coatings deposited on the inner wall of fused-silica capillaries and their influence on capillary electrophoresis (CE) performance of these coated columns is investigated. To carry out this study, a reproducible procedure to obtain capillaries with similar extent of modification of the surface silanols with 7-oct-1-enyltrimethoxisilane was first approached. Next the polymer attachment to the silica wall, via covalent linkage to the silyl reagent grafted onto the silica, was investigated. In this way, by using columns with a similar silylation extent, differences in CE performance observed among capillaries coated under diverse conditions could be assigned to the characteristics of the polyacrylamide layer. It is demonstrated that the characteristics and reproducibility of these polymeric coatings depend on the adequate control of both the temperature of polymerization and the degassing of the polymerizing dissolutions used. More interestingly, it is also demonstrated that the quantities of monomer (acrylamide), initiator (ammonium persulfate) and activator ( N, N, N′, N′-tetramethylethylenediamine), and the ratio among them used in the preparation of the coating polymer have a large influence on the performance of CE columns. The optimum conditions for preparing the polyacrylamide coatings are discussed. The applicability of these linear polyacrylamide-coated capillaries to the separation of basic and acidic proteins in free zone CE is demonstrated. Besides, the use of these coated columns in capillary gel electrophoresis for the separation of DNA fragments is shown.

Separation of disaccharides by affinity capillary electrophoresis in lectin-containing electrophoretic solutions.

Separation of the 1-phenyl-3-methyl-5-pyrazolone (PMP) derivatives of simple disaccharides (maltose, cellobiose, gentiobiose, lactose, and melibiose) by affinity capillary electrophoresis was investigated using lectin-containing neutral phosphate buffers, filled in a linear polyacrylamide-coated capillary. When Lens culinaris agglutinin (LCA) was added, the derivatives of glucobioses were retarded with varying magnitudes depending on the amount of LCA and were well separated from each other and from galactosyl glucose under optimized conditions. Addition of Ricinus communis 60 kDa agglutinin (RCA60) to the phosphate buffer gave a different migration profile, in which the derivatives of galactosyl glucoses were more retarded than those of glucobioses. However, addition of either lectin did not accomplish complete separation of the derivatives of all these disaccharides even under optimum conditions. The addition of two kinds of lectins in appropriate proportions improved separation. Thus, the binary system composed of LCA and RCA60, as well as LCA and soybean agglutinin from Glycine max (SBA), gave better separation of these derivatives, giving peak tops for all derivatives.