Multiplexed on-column protein digestion and capillary electrophoresis for high-throughput comprehensive peptide mapping

Peptide mapping of proteins by capillary electromigration methods

This review article provides a wide overview of important developments and applications of capillary electromigration methods in the area of peptide mapping of proteins in the period 1997-mid-2022, including review articles on this topic. It deals with all major aspects of peptide mapping by capillary electromigration methods: i) precleavage sample preparation involving purification, preconcentration, denaturation, reduction and alkylation of protein(s) to be analyzed, ii) generation of peptide fragments by off-line or on-line enzymatic and/or chemical cleavage of protein(s), iii) postcleavage preparation of the generated peptide mixture for capillary electromigration separation, iv) separation of the complex peptide mixtures by one-, two- and multidimensional capillary electromigration methods coupled with mass spectrometry detection, and v) a large application of peptide mapping for variable purposes, such as qualitative analysis of monoclonal antibodies and other protein biopharmaceuticals, monitoring of posttranslational modifications, determination of primary structure and investigation of function of proteins in biochemical and clinical research, characterization of proteins of variable origin as well as for protein and peptide identification in proteomic and peptidomic studies.

Ultrafast enzymatic digestion of proteins by microdroplet mass spectrometry

Enzymatic digestion for protein sequencing usually requires much time, and does not always result in high sequence coverage. Here we report the use of aqueous microdroplets to accelerate enzymatic reactions and, in particular, to improve protein sequencing. When a room temperature aqueous solution containing 10 µM myoglobin and 5 µg mL⁻¹ trypsin is electrosonically sprayed (−3 kV) from a homemade setup to produce tiny (∼9 µm) microdroplets, we obtain 100% sequence coverage in less than 1 ms of digestion time, in sharp contrast to 60% coverage achieved by incubating the same solution at 37 °C for 14 h followed by analysis with a commercial electrospray ionization source that produces larger (∼60 µm) droplets. We also confirm the sequence of the therapeutic antibody trastuzumab (∼148 kDa), with a sequence coverage of 100% for light chains and 85% for heavy chains, demonstrating the practical utility of microdroplets in drug development.

Mass spectrometry (MS)-based protein sequencing usually relies on in-solution proteolytic digestion, which is time-consuming and inefficient for certain proteins. Here, the authors achieve full protein sequence coverage in less than 1 ms by subjecting protein-protease mixtures to electrosonic spray ionization-MS.

Offline comprehensive liquid chromatography in combination with a Deoxyribonuclease I immobilized enzymatic reactor for selective screening of oligonucleotide mixtures

The development of a comprehensive ion-pair chromatography-immobilized enzyme reactor×ion-pair chromatography (IPC-IMER×IPC) methodology for the advanced characterization of DNA/RNA oligonucleotides (ONs) mixtures has been carried out. More in detail, a DNase I IMER has been coupled to IPC in the post column configuration, followed by the collection of the eluting fractions and reanalysis by IPC. The effect of the mobile phase over the IMER activity was qualitatively evaluated. The methodology proved to generate relevant ON degradation profiles that might be correlated with the ON stability towards nucleases. Moreover, this platform shows potential for its further implementation in selective analysis of ON mixtures and in mapping studies.

Insight into Trypsin Miscleavage: Comparison of Kinetic Constants of Problematic Peptide Sequences

Trypsin, a high fidelity protease, is the most widely used enzyme for protein digestion in proteomic research. Optimal digestion conditions are well-known and so are the expected cleavage products. However, missed cleavage sites are frequently observed when acidic amino acids, aspartic and glutamic acids, are present near the cleavage site. Also, the sequence motifs with successive lysine and/or arginine residues represent a source of missed cleaved sites. In spite of an adverse role of missed cleaved peptides on proteomic research, the digestion kinetics of these problematic sequences is not well-known. In this work, synthetic peptides with various sequence motifs were used as trypsin substrates. Cleavage products were analyzed with reversed-phase high performance liquid chromatography, and the kinetic constants for selected missed cleavage sites were calculated. Relative digestion speed for lysine and arginine sites is compared, including the digestion motifs flanked with aspartic and glutamic acid. Our findings show that DK and DTR motifs are cleaved by trypsin with 3 orders of magnitude lower speed than the arginine site. These motifs are likely to produce missed cleavage peptides in protein tryptic digests even at prolonged digestion times.

Analysis of identity, charge variants, and disulfide isomers of monoclonal antibodies with capillary zone electrophoresis in an uncoated capillary column

A set of related capillary zone electrophoresis (CZE) methods have been developed for the analysis of identity, charge variants, and disulfide isoforms of IgG monoclonal antibodies (mAbs). These methods utilize an uncoated capillary column. The combined use of concentrated zwitterionic (e-amino-caproic acid) buffer and acid flushing was effective in minimizing the adsorption of protein to the inner wall of a bare capillary. Under these conditions, a selective and reproducible separation of multiple IgG1 and IgG2 monoclonal antibodies (mAbs) was obtained with a long capillary column (40 cm effective length), allowing the reliable identification of different mAbs by migration time. A rapid ( approximately 10 min) and selective separation of charged variants of IgG mAbs was attained using a short capillary column (10 cm effective length). Finally, the addition of urea in the separation buffer resulted in the separation of disulfide isoforms of IgG2 mAbs by CZE. CZE methods using an uncoated capillary column offer a versatile, generic, and economical approach to the evaluation of identity, charge heterogeneity, and disulfide isoforms of IgG antibodies.

Coaxial flow system for chemical cytometry

Over the past decade, chemical cytometry performed by capillary electrophoresis (CE) has become increasingly valuable as a bioanalytical tool to quantify analytes from single cells. However, extensive use of CE-based chemical cytometry has been hindered by the relatively low throughput for the analysis of single adherent cells. In order to overcome the low throughput of CE-based analysis of adherent cells and increase its utility in evaluating cellular attributes, new higher throughput methods are needed. Integration of a coaxial buffer exchange system with CE-based chemical cytometry increased the rate of serial analyses of cells. In the designed system, fluid flow through a tube coaxial to the separation capillary was used to supply electrophoretic buffer to the capillary. This sheath or coaxial fluid was turned off between analysis of cells and on during cell sampling and electrophoresis. Thus, living cells were not exposed to the nonphysiologic electrophoretic buffer prior to lysis. Key parameters of the system such as the relative capillary-sheath positions, buffer flow velocities, and the cell chamber design were optimized. To demonstrate the utility of the system, rat basophilic leukemic cells loaded with Oregon green and fluorescein were serially lysed and loaded into a capillary. Separation of the contents of 20 cells at a rate of 0.5 cells/min was demonstrated.

Electrophoretically mediated microanalysis of a nicotinamide adenine dinucleotide-dependent enzyme and its facile multiplexing using an active pixel sensor UV detector

An electrophoretically mediated microanalysis (EMMA) method has been developed for yeast alcohol dehydrogenase and quantification of reactant and product cofactors, NAD and NADH. The enzyme substrate ethanol (1% (v/v)) was added to the buffer (50 mM borate, pH 8.8). Results are presented for parallel capillary electrophoresis with a novel miniature UV area detector, with an active pixel sensor imaging an array of two or six parallel capillaries connected via a manifold to a single output capillary in a commercial CE instrument, allowing conversions with five different yeast alcohol dehydrogenase concentrations to be quantified in a single experiment.

A simple peptide mapping method by partial filling micellar electrokinetic capillary chromatography with a zwitterionic–nonionic mixed micelle

A partial filling micellar electrokinetic capillary chromatography (PF-MEKC) method with a mixed micelle system composed of a zwitterionic surfactant named 3-(N,N-dimethylhexadecylammonium)propanesulfonate (PAPS) and a nonionic surfactant polyethylene glycol dodecyl ether (Brij 35) for peptide mapping is described. The method was demonstrated by the separation of tryptic digestion of bovine serum albumin (BSA). The optimal mixed micelle solution was 50 mM NH(4)OH-HCOOH buffer (pH 2.0) containing 32 mM PAPS and 0.6% (m/v) Brij 35. It was found that the mixed micelle system permitted a highly selective separation of the tryptic digestion. The high separation selectivity was probably due to the ion-pairing interaction between the zwitterionic surfactant molecules and the peptides.

Capillary electrophoresis at the omics level: Towards systems biology

Emerging systems biology aims at integrating the enormous amount of existing omics data in order to better understand their functional relationships at a whole systems level. These huge datasets can be obtained through advances in high-throughput, sensitive, precise, and accurate analytical instrumentation and technological innovation. Separation sciences play an important role in revealing biological processes at various omic levels. From the perspective of systems biology, CE is a strong candidate for high-throughput, sensitive data generation which is capable of tackling the challenges in acquiring qualitative and quantitative knowledge through a system-level study. This review focuses on the applicability of CE to systems-based analytical data at the genomic, transcriptomic, proteomic, and metabolomic levels.

Fast on-column protein digestion with subsequent peptide mapping using tandem mass spectrometry with information dependent acquisition

A platform for rapid on-line protein digestion of protein mixtures for direct infusion to a mass spectrometer is presented. A mixture of protein A, staphylococcal enterotoxin B and cytochrome c was used as a model mixture injected on a gel filtration column and a trypsin reactor which were connected in series to a micro liquid chromatography (microLC) system. The peptides in the column eluate were analyzed with ESI tandem mass spectrometry, utilizing information dependent acquisition (IDA). In one step, the proteins in the mixture (microM concentrations) were concomitantly desalted, separated, digested and identified with an overall analysis time of less than 40 min. Protein sequence coverage of 78-95% for the involved substances was achieved.

Techniques for high-throughput characterization of peptides, oligonucleotides and catalysis efficiency

Combinatorial processes have been widely applied to many disciplines in chemistry and biology. The vast numbers of unique entities generated by combinatorial synthesis have led to the development of high-throughput methods for characterizing samples, to avoid bottlenecks created by the application of conventional, serial-based analytical techniques. In recent years, high-throughput and novel methods utilizing mass spectrometry, multiplexed capillary electrophoresis, various forms of optical detection, and even sound waves have been investigated for a variety of applications.

Automated analysis of individual particles using a commercial capillary electrophoresis system

Capillary electrophoretic analysis of individual submicrometer size particles has been previously done using custom-built instruments. Despite that these instruments provide an excellent signal-to-noise ratio for individual particle detection, they are not capable of performing automated analyses of particles. Here we report the use of a commercial Beckman P/ACE MDQ capillary electrophoresis (CE) instrument with on-column laser-induced fluorescence (LIF) detection for the automated analysis of individual particles. The CE instrument was modified with an external I/O board that allowed for faster data acquisition rates (e.g. 100 Hz) than those available with the standard instrument settings (e.g. 4 Hz). A series of eight hydrodynamic injections expected to contain 32 +/- 6 particles, each followed by an electrophoretic separation at -300 V cm(-1) with data acquired at 100 Hz, showed 28 +/- 5 peaks corresponding to 31.9 particles as predicted by the statistical overlap theory. In contrast, a similar series of hydrodynamic injections followed by data acquisition at 4 Hz revealed only 8 +/- 3 peaks suggesting that the modified system is needed for individual particle analysis. Comparison of electropherograms obtained at both data acquisition rates also indicate: (i) similar migration time ranges; (ii) lower variation in the fluorescence intensity of individual peaks for 100 Hz; and (iii) a better signal-to-noise ratio for 4 Hz raw data. S/N improved for 100 Hz when data were smoothed with a binomial filter but did not reach the S/N values previously reported for post-column LIF detection. The proof-of-principle of automated analysis of individual particles using a commercially available CE system described here opens exciting possibilities for those interested in the study and analyses of organelles, liposomes, and nanoparticles.