Surfing silica surfaces superciliously

CE-MS for Proteomics and Intact Protein Analysis

This chapter aims to explore various parameters involved in achieving high-end capillary electrophoresis hyphenated to mass spectrometry (CE-MS) analysis of proteins, peptides, and their posttranslational modifications. The structure of the topics discussed in this book chapter is conveniently mapped on the scheme of the CE-MS system itself, starting from sample preconcentration and injection techniques and finishing with mass analyzer considerations. After going through the technical considerations, a variety of relevant applications for this analytical approach are presented, including posttranslational modifications analysis, clinical biomarker discovery, and its growing use in the biotechnological industry.

Novel approach for the synthesis of a neutral and covalently bound capillary coating for capillary electrophoresis-mass spectrometry made from highly polar and pH-persistent N-acryloylamido ethoxyethanol

Statically adsorbed or covalently coupled capillary coatings are of crucial importance in capillary electrophoresis-mass spectrometry for the separation of peptides and proteins. So far, published coating strategies and commercially available coated capillaries have a limited pH-stability so that the analysis at strongly acidic pH is limited, or harsh rinsing procedures for biological sample analysis cannot be applied. We here present a capillary coating based on Si-C linkages to N-acryloylamido ethoxyethanol (AAEE) with a new synthetic strategy including LiAlH₄ surface reaction. We optimized the coating method with emphasis on stability and reproducibility applying harsh rinsing procedures (strong acid, strong base and organic solvent), using the electroosmotic mobility and separation efficiency of tryptic peptides as performance measure. Complete synthesis is performed in less than 2 days for up to 8 capillaries in parallel of more than 16 m total length. Intra- and inter-batch reproducibility were determined regarding electroosmotic mobility, separation efficiency and migration time precision in CE-MS separations of tryptically digested bovine serum albumin. Coating stability towards rinsing with strong acid (1 mol/L HCl), organic solvent (acetonitrile) and strong base (1 mol/L NaOH) was investigated. Outstanding performance was found for single capillaries. However, inter-capillary reproducibility is discussed critically. The new coating was successfully applied for reproducible CE-MS separation of large proteins in diluted serum, medium-sized peptides and small and highly charged polyamines in fish egg extracts using a very acidic background electrolyte containing 0.75 mol/L acetic acid and 0.25 mol/L formic acid (pH 2.2).

Comparison of three modifications of fused-silica capillaries and untreated capillaries for protein profiling of maize extracts by capillary electrophoresis

In this work, capillary electrophoresis was applied to protein profiling of fractionated extracts of maize. A comparative study on the application of uncoated fused-silica capillaries and capillaries modified with hydroxypropylmethylcellulose, ω-iodoalkylammonium salt and a commercially available neutral capillary covalently coated with polyacrylamide is presented. The coating stability, background electrolyte composition, and separation efficiency were investigated. It was found that for zeins separation, the most stable and efficient was the capillary coated with polyacrylamide. Finally, the usefulness of these methods was studied for the differentiation of zein fraction in transgenic and nontransgenic maize. Zeins extracted from maize standards containing 0 and 5% m/m genetic modification were successfully separated, but slight differences were observed in terms of the zein content. Albumin and globulin fractions were analyzed with the use of unmodified fused-silica capillary with borate buffer pH 9 and the capillary coated with polyacrylamide with phosphate buffer pH 3. In the albumin fraction, additional peaks were found in genetically modified samples.

Recent advances in electrophoretic techniques for the characterization of protein biomolecules: a poker of aces

The four classical modes of electrophoresis of protein molecules (sodium dodecyl sulphate electrophoresis, SDS-PAGE, isoelectric focusing, IEF, and immobilized pH gradients, IPGs, two-dimensional maps, 2D, and capillary electrophoresis, CE) are here reviewed, with special emphasis on recent innovations. Thus, in the case of SDS-PAGE, a novel method, consisting in focusing SDS-protein micelles against a gradient of cationic charges grafted onto a polyacrylamide gel is presented. In the case of IEF, the recent decoding of the structure, polydispersity, molecular mass distribution and buffering properties of the soluble carrier ampholyte buffers are here discussed. In regard to two dimensional mapping, recent instrumentation for performing 2D maps in horizontal, large gel slabs (up to 30 cm × 40 cm) and in a radial format for the SDS dimension is here evaluated. Finally, in the case of CE, three major applications are presented: a thorough study of capillary IEF and of all experimental variables, a method of importance in screening of rDNA products; the possibility of running proteins and peptide separations in very acidic, amphoteric, isoelectric buffers in absence of any capillary coating; finally, the possibility of producing a facile, user friendly, covalent coating of the wall silanols via bonding of quaternarized piperazines endowed with an iodinated tail. In acidic, volatile buffers, such protein/peptide runs can be directly interfaced with mass spectrometry instrumentation.

Pressurized CEC of neutral and charged solutes using silica monolithic stationary phases functionalized with 3-(2-aminoethylamino)propyl ligands

A novel silica monolithic stationary phase functionalized with 3-(2-aminoethylamino)propyl ligands for pressurized CEC has been presented. The monolithic capillary columns were prepared by a sol-gel process in 75 microm id fused-silica capillaries and followed by a chemical modification. The diamino groups on the surface of the stationary phase are meant to generate the chromatographic surface and a substantial anodic EOF as well as to provide electrostatic interaction sites for charged solutes. The electrochromatographic characterization and column performance were evaluated by a variety of neutral and charged solutes. It was observed that the anodic EOF for the diamine-bonded monolith was greatly affected by the reaction time with 3-(2-aminoethylamino)propyltrimethoxysilane and the PEG amount in the sol-gel reaction mixture in addition to the mobile phase conditions. The monolithic stationary phase exhibited hydrophilic interaction chromatographic behavior toward neutral solutes. Good separations of various solutes including phenols, nucleic acid bases, nucleosides and nucleotides were achieved under different experimental conditions. Fast and efficient separations were obtained with high plate counts reaching more than 130,000 plates/m.

Isotope-coded two-dimensional maps: tagging with deuterated acrylamide and 2-vinylpyridine

Isotope-coded two-dimensional maps, with either D(0)/D(3)-acrylamide or D(0)/D(4) 2-vinyl pyridine, are described in detail. They have the advantage of running the two samples under investigation within a single slab gel, thus minimizing errors because of spot matching with software packages when samples are run in parallel maps. Labeling with deuterated acrylamide is very simple and inexpensive, because this chemical is commercially available. The experiment has to be carried out at alkaline pH values (pH 8.5-9.0) and with high molarities of alkylating agent (50-100 mM) to ensure good conversion efficiency. On the contrary, labeling with 2-vinyl pyridine (2-VP) can be performed in much lower alkylant molarities (20 mM) and at neutral pH values, thus ensuring essentially 100% conversion efficiency coupled with 100% specificity, because the reaction is sustained by the partial positive and negative charges on the 2-VP and -SH group, respectively. However, deuterated 2-VP is not commercially available and it has to be synthesized ad hoc.

Determination of oxalyl-coenzyme A decarboxylase activity in Oxalobacter formigenes and Lactobacillus acidophilus by capillary electrophoresis

Oxalyl-coenzyme A decarboxylase (OXC) is a key enzyme in the catabolism of the highly toxic oxalate, catalysing the decarboxylation of oxalyl-coenzyme A (Ox-CoA) to formyl-coenzyme A (For-CoA). In the present study, a capillary electrophoretic (CE) method was proposed for the assessment of the activity of recombinant OXC from two bacteria, namely Oxalobacter formigenes DSM 4420 and Lactobacillus acidophilus LA 14. In particular, the degradation of the substrate Ox-CoA occurring in the enzymatic reaction could be monitored by the off-line CE method. A capillary permanently coated with polyethylenimine (PEI) was used and in the presence of a neutral background electrolyte (50 mM phosphate buffer at pH 7.0), a reversal of the electroosmotic flow was obtained. Under these conditions, the anodic migration of Ox-CoA (substrate) and For-CoA (reaction product) occurred and their separation was accomplished in less than 12 min. The CE method was validated for selectivity, linearity (range of Ox-CoA within 0.005-0.650 mM), sensitivity (LOD of 1.5 microM at the detection wavelength of 254 nm), precision and accuracy. Steady state kinetic constants (V(max), K(m) or k') of OXC were finally estimated for both the bacteria showing that although L. acidophilus LA 14 provided a lower oxalate breakdown than O. formigenes DSM 4420, it could be a potentially useful probiotic in the prevention of diseases related to oxalate.

High throughput analysis of tryptophan metabolites in a complex matrix using capillary electrophoresis coupled to time-of-flight mass spectrometry

A capillary electrophoresis method for separation and detection with time-of-flight mass spectrometry is described for tryptophan metabolites in the kynurenic pathway. Tryptophan metabolites are usually difficult to detect with electrospray mass spectrometry since they have low surface activity and occur in low nanomolar to micromolar range in body fluids. Modification of the silica-wall with 1-(4-iodobutyl)4-aza-1-azoniabicyclo[2,2,2]octane iodide, also named M7C4I, has successfully been used to deactivate the fused silica wall and generate a stable reversed electroosmotic flow. Utilizing this advantage together with electrospray ionization time-of-flight mass spectrometry, which generates high resolution and fast acquisition monitoring of species, proved to be successful even for such a complex matrix like human cerebrospinal fluid.

Control of the EOF in CE using polyelectrolytes of different charge densities

The control of the EOF direction and magnitude remains one of the more challenging issues for the optimization of separations in CE. In this work, we investigated the possibility to use variously charged polyanions for a fine-tuning of the EOF using polyelectrolyte multilayers. For that purpose, polyanions of poly(acrylamide-co-2-acrylamido-2-methyl-1-propanesulfonate) (PAMAMPS) with different chemical charge rates varying between 3 and 100% were used. These copolymers are statistic hydrophilic copolymers of acrylamide (AM) and 2-acrylamido-2-methyl-1-propanesulfonate (AMPS). The study of the influence of the chemical charge rate (AMPS molar proportion in the copolymer) on the electroosmotic mobility (mu(eo)) of a capillary modified by a polyelectrolyte bilayer (polycation/PAMAMPS) revealed that the fine-tuning of the EOF was possible, at least for cathodic or slightly anodic EOF (micro(eo) from -5 x 10(-5) to +35 x 10(-5) cm(2)V(-1)s(-1)). Electroosmotic mobility values were compared with the free-draining electrophoretic mobilities of the PAMAMPS constituting the last layer of the capillary coating. The stability of the EOF is discussed in detail on the basis of successive determinations of electroosmotic mobility and migration times. The application to the separation of a model peptide mixture demonstrated the interest (and the simplicity) of this approach for optimizing resolution and analysis time. Experimental resolutions were compared to the theoretical ones that we would obtain on a fused-silica capillary having the same EOF as the coated capillary.

Effect of barium tetraborate on the separation of tryptic digests of proteins by zone electrophoresis in uncoated capillaries

A simple, fast, efficient and reproducible method for peptide separations in CZE is reported. It consists in running tryptic digests of peptides in an uncoated capillary, in a BGE composed of tetraborate as a buffering ion, in which the typical sodium counterion is substituted with barium. Efficient absorption of this divalent cation to ionized silanols and barium silicate precipitation seem to be able to shield effectively the silica surface from separands. This is demonstrated by the fact that, when tBa(2+) ions are present in solution (from pH 8.5 up to pH 11.0), the electroendoosmotic flow is reversed; such reversal being progressively higher at higher pH values, by up to a four-fold. Separations become progressively better at higher pH values, whereas at pH 11 in sodium tetraborate they are dramatically worsened. It is further hypothesized that the barium silicate layer further protects the silica surface against dissolution and corrosion which is quite substantial at pH 11.

Capillary electrophoresis-based separation techniques for the analysis of proteins

CE offers the advantages of high speed, great efficiency, as well as the requirement of minimum amounts of sample and buffer for the analysis of proteins. In this review, we summarize the CE-based techniques coupled with absorption, LIF, and MS detection systems for the analysis of proteins mostly within the past 5 years. The basic principle of each technique and its advantages and disadvantages for protein analysis are discussed in brief. Advanced CE techniques, including on-column concentration techniques and high-efficiency multidimensional separation techniques, for high-throughput protein profiling of complex biological samples and/or of single cells are emphasized. Although the developed techniques provide improved peak capacity, they have not become practical tools for proteomics, mainly because of poor reproducibility, low-sample lading capacity, and low throughput due to ineffective interfaces between two separation dimensions and that between separation and MS systems. In order to identify the complexities and dynamics of the proteomes expressed by cells, tissues, or organisms, techniques providing improved analytical sensitivity, throughput, and dynamic ranges are still demanded.

Organic and inorganic di-cations for capillary silica coating and EOF modulation in CE: Example of application in PEG analysis

EOF measurements, by using 1,4-di-(4-aza-1-azonia-bicyclo[2.2.2]octane)butane diiodide, barium and strontium tetraborate as silica wall modifiers, are reported and, as an example of application, analysis of PEG (PEG 400-2000) polydisperse preparations in free solution CZE is shown. PEGs have been derivatized with phthalic anhydride so as to form singly or doubly charged derivatives with strong UV absorbance at 214 nm. Whereas separations in plain tetraborate buffer, pH 9.0, without any EOF control, did not lead to good resolution of all-size oligomers and suffered from long analysis times, excellent resolution of all oligomers up to 40 ethylene oxide (EO) units could be obtained under EOF control. Such EOF modulation was engendered by addition of 1 mM M7C4M7, a doubly charged organic cation able to stick tenaciously to the silica wall. Further modulation of EOF and silica surface modification could be achieved also by addition of inorganic cations, notably those of group II, whereas monovalent cations did not seem to affect much the EOF flux. Among the doubly charged cations investigated, Ca++, Mg++, Sr++ and Ba++, the latter did seem to offer best EOF control and reproducible runs. A judicious blend of M7C4M7 (0.33-1 mM range) with barium (10-20 mM range) allowed baseline resolution of all PEG oligomers investigated up to PEG 2000 and >40 EO units in length. In this last case, best results in terms of reproducibility and separation efficiency of the more heavy homologues were obtained using Li+ salt in small amounts.

Recent developments in capillary electrophoresis and capillary electrochromatography of peptides

The article gives a comprehensive review on the recent developments in the applications of high-performance capillary electromigration methods, 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, covers the methodological aspects of capillary electroseparations of peptides, such as rational selection of separation conditions, sample preparation, suppression of peptide adsorption, 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, purity control, determination in biomatrices, monitoring of chemical and enzymatical reactions and physical changes, 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.

Comprehensive Protein Profiling by Multiplexed Capillary Zone Electrophoresis Using Cross-Linked Polyacrylamide Coated Capillaries

We have recently developed a new process to create cross-linked polyacrylamide (CPA) coatings on capillary walls to suppress protein-wall interactions. Here, we demonstrate CPA-coated capillaries for high-efficiency (>2 x 10(6) plates per meter) protein separations by capillary zone electrophoresis (CZE). Because CPA virtually eliminates electroosmotic flow, positive and negative proteins cannot be analyzed in a single run. A "one-sample-two-separation" approach is developed to achieve a comprehensive protein analysis. High throughput is achieved through a multiplexed CZE system.

Utilizing the pH hysteresis effect for versatile and simple electrophoretic analysis of proteins in bare fused-silica capillaries

The analysis of peptides and proteins by CE is often desirable due to low sample consumption and possibilities for nondenaturing yet highly effective separations. However, adsorption to the inner surfaces of fused-silica capillaries often is detrimental to such analyses. This phenomenon is especially pronounced in the analysis of basic proteins and proteins containing exposed positively charged patches. To avoid wall interactions numerous buffer additives and static and dynamic wall coating principles have been devised. We previously showed (J. Chromatogr. A 2004, 1059, 215-222) that CE of the basic protein beta2-glycoprotein was rendered possible by an acidic pretreatment step, and we attributed this observation to the so-called pH hysteresis effect that influences the time for pH equilibration of the capillary wall and thus the effective wall charge and the electroosmotic mobility. We here investigate the effects of different pretreatment techniques on EOF values and on the rate of the deprotonation of silanol groups when performing the electrophoresis at neutral pH. We show the utility of this simple approach for the CE analysis of a number of basic proteins in plain silica capillaries at physiological pH.

Combining capillary electrophoresis with mass spectrometry for applications in proteomics

Mass spectrometry (MS)-based proteomics is currently dominated by the analysis of peptides originating either from digestion of proteins separated by two-dimensional gel electrophoresis (2-DE) or from global digestion; the simple peptide mixtures obtained from digestion of gel-separated proteins do not usually require further separation, while the complex peptide mixtures obtained by global digestion are most frequently separated by chromatographic techniques. Capillary electrophoresis (CE) provides alternatives to 2-DE for protein separation and alternatives to chromatography for peptide separation. This review attempts to elucidate how the most promising CE modes, capillary zone electrophoresis (CZE) and capillary isoelectric focusing (CIEF), might best be applied to MS-based proteomics. CE-MS interfacing, mass analyzer performance, column coating to minimize analyte adsorption, and sample stacking for CZE are considered prior to examining numerous applications. Finally, multidimensional systems that incorporate CE techniques are examined; CZE often finds use as a fast, final dimension before ionization for MS, while CIEF, being an equilibrium technique, is well-suited to being the first dimension in automated fractionation systems.