Recent developments in capillary and microchip electroseparations of peptides (2021-mid-2023)

This review article brings a comprehensive survey of developments and applications of high-performance capillary and microchip electromigration methods (zone electrophoresis in a free solution or in sieving media, isotachophoresis, isoelectric focusing, affinity electrophoresis, electrokinetic chromatography, and electrochromatography) for analysis, micropreparation, and physicochemical characterization of peptides in the period from 2021 up to ca. the middle of 2023. Progress in the study of electromigration properties of peptides and various aspects of their analysis, such as sample preparation, adsorption suppression, electroosmotic flow regulation, and detection, are presented. New developments in the particular capillary electromigration methods are demonstrated, and several types of their applications are reported. They cover qualitative and quantitative analysis of synthetic or isolated peptides and determination of peptides in complex biomatrices, peptide profiling of biofluids and tissues, and monitoring of chemical and enzymatic reactions and physicochemical changes of peptides. They include also amino acid and sequence analysis of peptides, peptide mapping of proteins, separation of stereoisomers of peptides, and their chiral analyses. In addition, micropreparative separations and physicochemical characterization of peptides and their interactions with other (bio)molecules by the above CE methods are described.

Recent developments in capillary and microchip electroseparations of peptides (2019-mid 2021)

The review provides a comprehensive overview of developments and applications of high performance capillary and microchip electroseparation methods (zone electrophoresis, isotachophoresis, isoelectric focusing, affinity electrophoresis, electrokinetic chromatography, and electrochromatography) for analysis, microscale isolation, and physicochemical characterization of peptides from 2019 up to approximately the middle of 2021. Advances in the investigation of electromigration properties of peptides and in the methodology of their analysis, such as sample preparation, sorption suppression, EOF control, and detection, are presented. New developments in the individual CE and CEC methods are demonstrated and several types of their applications are shown. They include qualitative and quantitative analysis, determination in complex biomatrices, monitoring of chemical and enzymatic reactions and physicochemical changes, amino acid, sequence, and chiral analyses, and peptide mapping of proteins. In addition, micropreparative separations and determination of significant physicochemical parameters of peptides by CE and CEC methods are described.

CEToolbox: Specialized calculator for capillary electrophoresis users as an android application

CE has been demonstrated to be a useful and powerful separation method for the characterization of charged and neutral molecules. Since the end of the 1980s and the development of the first commercialized CE device, the use of this separation method has continued to grow for academic and industrial research involving inexorably increasing of the number of CE users. Whatever the application domain, each CE user is daily confronted to the same problems often based on basic calculations of separation properties. In order to help the community of CE users to get quickly and easily a lot of information, and desiring to provide a tool running on mobile platforms, CEToolbox has been developed as a free Android application. Within few clicks, CEToolbox offers extensive injection information as injected volume, total capillary volume, proportion and amount of injected sample, rinsing time, and electrical field. Moreover, three additional tabs allow to obtain the calculation of the viscosity and the conductivity of BGE, and the separation flow rates. Finally, a last tab is dedicated to the calculation of electroosmotic mobility and effective mobilities for a maximum of 20 compounds. CEToolbox, which can be downloaded for free on Google and F-Droid application stores, was developed to simplify the daily of CE users regardless of the CE devices.

Recent developments in capillary and microchip electroseparations of peptides (2015-mid 2017)

The review brings a comprehensive overview of recent developments and applications of high performance capillary and microchip electroseparation methods (zone electrophoresis, isotachophoresis, isoelectric focusing, affinity electrophoresis, electrokinetic chromatography, and electrochromatography) to analysis, microscale isolation, purification, and physicochemical and biochemical characterization of peptides in the years 2015, 2016, and ca. up to the middle of 2017. Advances in the investigation of electromigration properties of peptides and in the methodology of their analysis (sample preseparation, preconcentration and derivatization, adsorption suppression and EOF control, and detection) are described. New developments in particular CE and CEC methods are presented and several types of their applications to peptide analysis are reported: qualitative and quantitative analysis, determination in complex (bio)matrices, monitoring of chemical and enzymatical reactions and physical changes, amino acid, sequence and chiral analysis, and peptide mapping of proteins. Some micropreparative peptide separations are shown and capabilities of CE and CEC methods to provide important physicochemical characteristics of peptides are demonstrated.

Poly(N,N-Dimethylacrylamide)-Based Coatings to Modulate Electroosmotic Flow and Capillary Surface Properties for Protein Analysis

Capillary electrophoresis (CE) is one of the most powerful techniques for the separation of biomolecules. However, the separation efficiency of proteins in CE is often compromised by their tendency to interact with the silanol groups on the surface of the inner capillary and by an uncontrolled electroosmotic flow. Herein, we report on the use of novel hydrophilic polymeric coatings that can modulate the properties of the capillary walls. The novelty of these poly(N,N-dimethylacrylamide)-based copolymers relies on the simultaneous presence of chemically reactive groups (N-acryloyloxysuccinimide and glycidyl methacrylate) and silane groups in the backbone, which results in highly stable films due to the covalent reaction between the polymer and the glass silanols. A careful optimization of monomer concentration confers anti-fouling properties to the polymer coatings, and thus allows for highly efficient acidic and alkaline protein separations. Furthermore, the presence of these monomers makes it possible to modulate the electroosmotic flow from negligible to reduced values, depending on the desired application.

Separation of Peptides by Capillary Electrophoresis

Peptides are an important class of analytes in chemistry, biochemistry, food chemistry, as well as medical and pharmaceutical sciences including biomarker analysis in peptidomics and proteomics. As a high-resolution technique, capillary electrophoresis (CE) is well suited for the analysis of polar compounds such as peptides. In addition, CE is orthogonal to high-performance liquid chromatography (HPLC) as both techniques are based on different physicochemical separation principles. For the successful development of peptide separations by CE, operational parameters including puffer pH, buffer concentration and buffer type, applied voltage, capillary dimensions, as well as background electrolyte additives such as detergents, ion-pairing reagents, cyclodextrins, (poly)amines, and soluble polymers have to be considered and optimized.

On-Line Solid-Phase Extraction Capillary Electrophoresis Mass Spectrometry for Preconcentration and Clean-Up of Peptides and Proteins

One of the major drawbacks of capillary electrophoresis (CE) and other microscale separation techniques, for the analysis of low abundant peptides and proteins in complex samples, are the poor concentration limits of detection. Several strategies have been developed to improve CE sensitivity. Here, we describe an on-line solid-phase extraction capillary electrophoresis mass spectrometry method with a commercial C18 sorbent for clean-up and preconcentration of neuropeptides from highly diluted biological samples.

Advances in urinary proteome analysis and applications in systems biology

The urinary proteome is the focus of many studies due to the ease of urine collection and the relative proteome stability. Systems biology allows the combination of multiple omics studies, forming a link between proteomics, metabolomics, genomics and transcriptomics. In-depth data interpretation is achieved by bioinformatics analysis of -omics data sets. It is expected that the contribution of systems biology to the study of the urinary proteome will offer novel insights. The main focus of this review is on technical aspects of proteomics studies, available tools for systems biology analysis and the application of urinary proteomics in clinical studies and systems biology.

Ionic liquids as buffer additives in ionic liquid-polyacrylamide gel electrophoresis separation of mixtures of low and high molecular weight proteins

Three novel ionic liquids (ILs) [C_nPBr] (n= 4, 6, 8) have been synthesized and were used as buffer additives in IL-PAGE separation of mixture of acidic proteins.

Capillary electrophoresis separation of peptide diastereomers that contain methionine sulfoxide by dual cyclodextrin-crown ether systems

A dual-selector system employing achiral crown ethers in combination with cyclodextrins has been developed for the separation of peptide diastereomers that contain methionine sulfoxide. The combinations of the crown ethers 15-crown-5, 18-crown-6, Kryptofix® 21 and Kryptofix® 22 and β-cyclodextrin, carboxymethyl-β-cyclodextrin, and sulfated β-cyclodextrin were screened at pH 2.5 and pH 8.0 using a 40/50.2 cm, 50 μm id fused-silica capillary and a separation voltage of 25 kV. No diastereomer separation was observed in the sole presence of crown ethers, while only sulfated β-cyclodextrin was able to resolve some peptide diastereomers at pH 8.0. Depending on the amino acid sequence of the peptide and the applied cyclodextrin, the addition of crown ethers, especially the Krpytofix® diaza-crown ethers, resulted in significantly enhanced chiral recognition. Keeping one selector of the dual system constant, increasing concentrations of the second selector resulted in increased peak resolution and analyte migration time for peptide-crown ether-cyclodextrin combinations. The simultaneous diastereomer separation of three structurally related peptides was achieved using the dual selector system.

Analysis of monoclonal antibody by a novel CE-UV/MALDI-MS interface

mAbs are highly complex proteins that present a wide range of microheterogeneity that requires multiple analytical methods for full structure assessment and quality control. As a consequence, the characterization of mAbs on different levels is particularly product- and time-consuming. CE-MS couplings, especially to MALDI, appear really attractive methods for the characterization of biological samples. In this work, we report the last instrumental development and performance of the first totally automated off-line CE-UV/MALDI-MS/MS. This interface is based on the removal of the original UV cell of the CE apparatus, modification of the spotting device geometry, and creation of an integrated delivery matrix system. The performance of the method was evaluated with separation of five intact proteins and a tryptic digest mixture of nine proteins. Intact protein application shows the acquisition of electropherograms with high resolution and high repeatability. In the peptide mapping approach, a total number of 154 unique identified peptides were characterized using MS/MS spectra corresponding to average sequence coverage of 64.1%. Comparison with NanoLC/MALDI-MS/MS showed complementarity at the peptide level with an increase of 42% when using CE/MALDI-MS coupling. Finally, this work represents the first analysis of intact mAb charge variants by CZE using an MS detection. Moreover, using a peptide mapping approach CE-UV/MALDI-MS/MS fragmentation allowed 100% sequence coverage of the light chain and 92% of the heavy chain, and the separation of four major glycosylated peptides and their structural characterization.

Identification of bioactive peptides in hypoallergenic infant milk formulas by CE-TOF-MS assisted by semiempirical model of electromigration behavior

Biologically active peptides derived from complex bovine milk protein hydrolysates are of particular interest in food science and nutrition because they have been shown to play different physiological roles, providing benefits in human health. In this study, we used CE-TOF-MS for separation and identification of bioactive peptides in three hypoallergenic infant milk formulas. An appropriate sample cleanup using a citrate buffer with DTT and urea followed by SPE with Sep-Pack® C18 and StrataX™ cartridges allowed the detection of a large number of low molecular mass bioactive peptides. This preliminary identification was solely based on the measured experimental monoisotopic molecular mass values (M(exp)). Later, we evaluated the classical semiempirical relationships between electrophoretic mobility and charge-to-mass ratio (m(e) vs. q/M(α), α = 1/2 for the classical polymer model) to describe their migration behavior. The assistance of migration prediction proved to be useful to improve reliability of the identification, avoiding misinterpretations and solving some identity conflicts. After revision, the identity of 24, 30, and 38 bioactive peptides was confirmed in each of the three infant milk formulas. A significant number of these peptides were reported as inhibitors of angiotensin-converting enzyme, however, the presence of sequences with other biological activities such as antihypertensive, antithrombotic, hypocholesterolemic, immunomodulation, cytotoxicity, antioxidant, antimicrobial, antigenic, or opioid was also confirmed.

Recent developments in capillary and microchip electroseparations of peptides (2011-2013)

The review presents a comprehensive survey of recent developments and applications of capillary and microchip electroseparation methods (zone electrophoresis, ITP, IEF, affinity electrophoresis, EKC, and electrochromatography) for analysis, isolation, purification, and physicochemical and biochemical characterization of peptides. Advances in the investigation of electromigration properties of peptides, in the methodology of their analysis, including sample preseparation, preconcentration and derivatization, adsorption suppression and EOF control, as well as in detection of peptides, are presented. New developments in particular CE and CEC modes are reported and several types of their applications to peptide analysis are described: conventional qualitative and quantitative analysis, determination in complex (bio)matrices, monitoring of chemical and enzymatical reactions and physical changes, amino acid, sequence and chiral analysis, and peptide mapping of proteins. Some micropreparative peptide separations are shown and capabilities of CE and CEC techniques to provide relevant physicochemical characteristics of peptides are demonstrated.

Performing isoelectric focusing and simultaneous fractionation of proteins on a rotary valve followed by sodium dodecyl-polyacrylamide gel electrophoresis

In this technical note, we design and fabricate a novel rotary valve and demonstrate its feasibility for performing isoelectric focusing and simultaneous fractionation of proteins, followed by sodium dodecyl-polyacrylamide gel electrophoresis. The valve has two positions. In one position, the valve routes a series of capillary loops together into a single capillary tube where capillary isoelectric focusing (CIEF) is performed. By switching the valve to another position, the CIEF-resolved proteins in all capillary loops are isolated simultaneously, and samples in the loops are removed and collected in vials. After the collected samples are briefly processed, they are separated via sodium dodecyl-polyacrylamide gel electrophoresis (SDS-PAGE, the second-D separation) on either a capillary gel electrophoresis instrument or a slab-gel system. The detailed valve configuration is illustrated, and the experimental conditions and operation protocols are discussed.

Site-specific separation and detection of phosphopeptide isomers with pH-mediated stacking capillary electrophoresis-electrospray ionization-tandem mass spectrometry

This study reported a pH-mediated stacking CE coupled with ESI MS/MS method to determine the phosphorylation sites of three synthetic phosphopeptides containing structural isomers. These phosphopeptides mimic the phosphopeptides (amino acid residues 12-25) derived from the trypsin-digested products of human lamin A/C protein. The LODs were determined to be 118, 132 and 1240 fmol for SGAQASS(19)TpPL(22)SPTR, SGAQASS(19)TPL(22)SpPTR, and SGAQASS(19)TpPL(22)SpPTR, respectively. The established method was employed to analyze the phosphorylation sites of the trypsin-digested products of glutathione S-transferase-lamin A/C (1-57) fusion protein that had been phosphorylated in vitro by cyclin-dependent kinase 1. The results indicated that this method is feasible to specifically determine the phosphorylation site from phosphopeptide isomers in the trypsin-digested products of a kinase-catalyzed phosphoprotein, which should benefit the investigation of protein kinase-mediated cellular signal transduction.

Capillary electrophoresis-mass spectrometry for Peptide analysis: target-based approaches and proteomics/peptidomics strategies

In this chapter, the potential of capillary electrophoresis-mass spectrometry (CE-MS) for peptide analysis is demonstrated by the presentation of two different strategies typically followed in analysis of these biomolecules by CE-MS. The first one is a target-based approach and it is used to detect a toxic oligopeptide in a complex matrix. Namely, CE-MS using an ion trap MS analyzer is applied to detect and quantify γ-glutamyl-S-ethenyl-cysteine (GEC) bioactive dipeptide in a legume plant. The second one is a shotgun-like methodology used for proteomic analysis. Particularly, CE-MS using a time-of-flight MS analyzer is employed to investigate the substantial equivalence between a genetically modified (GM) variety of soybean and its conventional isogenic counterpart. These generic methods have broad applications for the analysis of peptides in a large variety of matrices, including applications in the area of proteomics and peptidomics.

Neuropeptide analysis with liquid chromatography-capillary electrophoresis-mass spectrometric imaging

Herein we report the first attempt of coupling multidimensional separations to matrix-assisted laser desorption/ionization (MALDI) mass spectrometric imaging detection. Complex neuropeptide mixtures extracted from crustaceans were first fractionated by reversed-phase liquid chromatography (RPLC), and then subjected to a capillary electrophoresis-mass spectrometric imaging platform. With a specific focus on orcokinin family neuropeptides, we demonstrated that these trace-level analytes from complex neural tissue samples can be fully separated from chemical noise and interfering components and visualized as mass spectrometric imaging signals. A total of 19 putative orcokinins were detected, with highly efficient separations within the family being achieved for the first time. The results indicate that two-dimensional separation coupling to mass spectrometric imaging can serve as a novel and powerful tool in proteomics and peptidomics studies.

Pressure-assisted capillary electrophoresis coupling with matrix-assisted laser desorption/ionization-mass spectrometric imaging for quantitative analysis of complex peptide mixtures

Herein, we report a pressure-assisted capillary electrophoresis-mass spectrometric imaging (PACE-MSI) platform for peptide analysis. This new platform has addressed the sample diffusion and peak splitting problems that appeared in our previous groove design, and it enables homogeneous deposition of the CE trace for high-throughput MALDI imaging. In the coupling of CE to MSI, individual peaks (m/z) can be visualized as discrete colored image regions and extracted from the MS imaging data, thus eliminating issues with peak overlapping and reducing reliance on an ultrahigh mass resolution mass spectrometer. Through a PACE separation, 46 tryptic peptides from bovine serum albumin and 150 putative neuropeptides from the pericardial organs of a model organism blue crab Callinectes sapidus were detected from the MALDI MS imaging traces, enabling a 4- to 6-fold increase of peptide coverage as compared with direct MALDI MS analysis. For the first time, quantitation with high accuracy was obtained using PACE-MSI for both digested tryptic peptides and endogenous neuropeptides from complex biological samples in combination with isotopic formaldehyde labeling. Although MSI is typically employed in tissue imaging, we show in this report that it offers a unique tool for quantitative analysis of complex trace-level analytes with CE separation. These results demonstrate a great potential of the PACE-MSI platform for enhanced quantitative proteomics and neuropeptidomics.