Peptide mapping of proteins by capillary electromigration methods

CZE-MS peptide mapping: To desalt or not to desalt?

BACKGROUND

In "shotgun" approaches involving high-performance liquid chromatography or capillary zone electrophoresis (CZE), matrix removal prior to sample analysis is considered as an indispensable tool. Despite the fact that CZE offers a high tolerance towards salts, most publications reported on the use of desalting. There seems to be no clear consensus on the utilization of desalting in the CZE-MS community, most probably due to the absence of works addressing the comparison of desalted and non-desalted digests. Our aim was to fill this research gap using protein samples of varying complexity in different sample matrices.

RESULTS

First, standard protein digests were analyzed to build the knowledge on the effect of sample clean-up by solid-phase extraction (SPE) pipette tips and the possible stacking phenomena induced by different sample matrices. Desalting led to a somewhat altered peptide profile, the procedure affected mostly the hydrophilic peptides (although not to a devastating extent). Nevertheless, desalting samples allowed remarkable stacking efficiency owing to their low-conductivity sample background, enabling a so-called field-amplified sample stacking phenomenon. Non-desalted samples also produced a stacking event, the mechanism of which is based on transient-isotachophoresis due to the presence of high-mobility ions in the digestion buffer itself. Adding either extra ammonium ions or acetonitrile into the non-desalted digests enhanced the stacking efficiency. A complex sample (yeast cell lysate) was also analyzed with the optimal conditions, which yielded similar tendencies.

SIGNIFICANCE

Based on these results, we propose that sample clean-up in the bottom-up sample preparation process prior to CZE-MS analysis can be omitted. The preclusion of desalting can even enhance detection sensitivity, separation efficiency or sequence coverage.

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.

A comprehensive review of capillary electrophoresis-based techniques for erythropoietin isoforms analysis

Different CE techniques have been used to analyze erythropoietin. These techniques have been shown to be effective in differentiating and quantifying erythropoietin isoforms, including natural and recombinant origins. This review provides a comprehensive overview of various capillary electrophoresis-based techniques used for the analysis of erythropoietin isoforms. The importance of erythropoietin in clinical practice and the necessity for the accurate analysis of its isoforms are first discussed. Various techniques that have been used for erythropoietin isoform analysis are then described. The main body of the review focuses on the different capillary electrophoresis-based methods that have been developed for erythropoietin isoform analysis, including capillary zone electrophoresis and capillary isoelectric focusing. The advantages and drawbacks of each method as well as their applications are discussed. Suggestions into the future directions of the area are also described.

Comparative study on the deamidation of three recombinant human insulins using capillary electrophoresis

The applicability of capillary zone electrophoresis (CZE) for the separation of different recombinant human insulins and their deamidated isoforms was studied. The high resolving power of CZE is demonstrated by its ability to separate insulin isoforms differing only by 0.984 Da (different-fold deamidated forms) and even components having the exacts same mass but slightly different shapes (same-fold deamidated forms). From among the several insulins available, humulin, glargine and glulisine were selected for our study because their sequences and chemical parameters are quite similar, however, the small differences present in their amino acid sequences influence the deamidation processes. Using a background electrolyte with basic pH was favourable not only for the separation of the different types of insulin but also for the separation of deamidated protein forms even in a bare fused silica capillary. The LOD values ranged between 0.6 - 0.93 mg/L and 2.17 - 4.37 mg/L for UV and ESI-MS detection, respectively. At -20 - -80 °C, the deamidation is minimal, but at temperatures above +5 °C deamidation is accelerated. At +5 °C only 1-fold deamidation forms could be observed for each insulin. Acidified samples incubated for 1-month at room temperature showed varying levels of deamidation: 1-fold, 1-2-fold and 1-2-3-fold forms for glargine, glulisine and humulin, respectively.