Online CIEF-ESI-MS in glycerol-water media with a view to hydrophobic protein applications

Capillary Isoelectric Focusing of Proteins and Peptides Using an In-Line cIEF-ESI Interface with Improved MS Characteristics

Intact protein analysis using mass spectrometry (MS) is an important technique to characterize and provide a comprehensive overview of protein complexity. It is also the basis of "top-down" approaches in proteomics to describe the proteoforms of single protein's post-translational modifications (PTMs). MS-based analysis of intact proteins benefits from high-resolution separations prior to electrospray ionization. Capillary isoelectric focusing (cIEF) is a high-resolution separation for proteins and peptides which is capable of separating proteoforms. MS detection coupled to cIEF can separate, detect, and characterize proteoforms at the molecular level. However, cIEF with MS detection is a compromised process. The concentration of ampholytes required for cIEF is mutually exclusive with mass spectrometer contamination. We have improved an online cIEF-ESI-MS interface to reduce (desalt) amino acid ampholytes in-line after cIEF and prior to electrospray ionization. In proof of principle experiments, >90% increase in area under the curve of the electropherograms was observed with the interface compared to without the interface. Protein standards including proteoforms of cytochrome C, myoglobin, and α-casein were separated and resolved with high reproducibility. The interface did not compromise the linearity of the cIEF pH gradient separations, achieving a high linearity with a R2 of 0.99. In addition, a tryptic digest of BSA demonstrates baseline resolution of peptides with as little as 0.02 pI unit difference and a full width at half-maximum average of 7.1 s.

Chemical Mobilization-Based Capillary Isoelectric Focusing-Mass Spectrometry Using the nanoCEasy Interface for Pharmaceutical Protein Analysis

Capillary isoelectric focusing (CIEF) coupled with electrospray ionization mass spectrometry (ESI-MS) is regarded as an outstanding approach for protein and proteoform analysis, combining a high-resolution separation technique and an enhanced detection technique. The few so-far developed CIEF-ESI-MS approaches exhibit limitations regarding sensitivity and separation performance. Here, we report a new generic methodology for CIEF-ESI-MS based on chemical mobilization, leading to highly efficient separation. This new integrated methodology relies on exchanging catholyte, initially introduced in the nanoCEasy interface in the focusing step, with sheath liquid (SL) in order to chemically mobilize the analytes into the ESI-MS system. The CIEF-MS method is evaluated by separation of a peptide set, model proteins, and monoclonal antibody charge variants. The effect of various parameters including master mixture composition, field strength, catholyte, SL composition, focusing time, and capillary conditions is optimized and discussed. Excellent separation performance can be achieved with a pI resolution down to 0.1 pH unit. The mobilization reproducibility is demonstrated with "migration time" RSDs below 10%. Additionally, the chemical mobilization is compared with the pressure assistance-chemical mobilization method, demonstrating that even a small pressure causes a strong decrease in separation performance, which clearly indicates the benefit of the chemical mobilization-based method. The applicability and separation power of the developed method are further exhibited by separation of Fc-conjugated insulins (mass = 62 kDa) differing in only one amino acid.

Capillary electrophoresis-mass spectrometry for protein analyses under native conditions: Current progress and perspectives

Native mass spectrometry is a rapidly emerging technique for fast and sensitive structural analysis of protein constructs, maintaining the protein higher order structure. The coupling with electromigration separation techniques under native conditions enables the characterization of proteoforms and highly complex protein mixtures. In this review, we present an overview of current native CE-MS technology. First, the status of native separation conditions is described for capillary zone electrophoresis (CZE), affinity capillary electrophoresis (ACE), and capillary isoelectric focusing (CIEF), as well as their chip-based formats, including essential parameters such as electrolyte composition and capillary coatings. Further, conditions required for native ESI-MS of (large) protein constructs, including instrumental parameters of QTOF and Orbitrap systems, as well as requirements for native CE-MS interfacing are presented. On this basis, methods and applications of the different modes of native CE-MS are summarized and discussed in the context of biological, medical, and biopharmaceutical questions. Finally, key achievements are highlighted and concluded, while remaining challenges are pointed out.

Recent advances (2019-2021) of capillary electrophoresis-mass spectrometry for multilevel proteomics

Multilevel proteomics aims to delineate proteins at the peptide (bottom-up proteomics), proteoform (top-down proteomics), and protein complex (native proteomics) levels. Capillary electrophoresis-mass spectrometry (CE-MS) can achieve highly efficient separation and highly sensitive detection of complex mixtures of peptides, proteoforms, and even protein complexes because of its substantial technical progress. CE-MS has become a valuable alternative to the routinely used liquid chromatography-mass spectrometry for multilevel proteomics. This review summarizes the most recent (2019-2021) advances of CE-MS for multilevel proteomics regarding technological progress and biological applications. We also provide brief perspectives on CE-MS for multilevel proteomics at the end, highlighting some future directions and potential challenges.

An improved capillary isoelectric focusing-mass spectrometry method for high-resolution characterization of monoclonal antibody charge variants

Routine and high-resolution characterization of monoclonal antibody (mAb) charge variants is vital for controlling mAb quality as therapeutics. Capillary isoelectric focusing-mass spectrometry (cIEF-MS) has emerged as a powerful tool for characterizing mAb charge variants because it can achieve high-resolution separation and highly sensitive detection of proteins. It provides much better identification of charge variants than the traditionally used cIEF-UV method. However, further improvement of cIEF-MS regarding stability and separation resolution is needed. Here, we improved the stability and enhanced separation resolution of automated cIEF-MS by bettering the quality of capillary neutral coating, reducing catholyte pH to 10 for cIEF-MS for the first time, and systematically optimizing the cIEF separation conditions. The improved cIEF-MS method was applied to characterize charge variants of three previously well characterized mAbs (NISTmAb, cetuximab, trastuzumab) and one tool mAb (mAb1). The charge variants of the studied mAbs were well resolved, and the majority of post-translational modifications (PTMs) found in those mAbs agreed with the literature. cIEF-MS analyses of mAb1 were capable of discovering ten charge variants with various interesting PTMs, such as PGK amidation, incomplete C-terminal lysine clipping, glycosylation, and deamination. cIEF-MS was successfully used for accurately determining the isoelectric points (pIs) of mAb1 charge variants via analyzing the pI markers and spiking in a standard protein (cytochrome c) to samples for migration time normalization, which is beneficial for evaluating pI-related pharmacokinetic properties. Our cIEF-MS agreed with and, in some cases (i.e., cetuximab and mAb1), outperformed cIEF-UV for detecting mAb charge variants.

A Mini Review on Capillary Isoelectric Focusing-Mass Spectrometry for Top-Down Proteomics

Mass spectrometry (MS)-based top-down proteomics (TDP) requires high-resolution separation of proteoforms before electrospray ionization (ESI)-MS and tandem mass spectrometry (MS/MS). Capillary isoelectric focusing (cIEF)-ESI-MS and MS/MS could be an ideal method for TDP because cIEF can enable separation of proteoforms based on their isoelectric points (pIs) with ultra-high resolution. cIEF-ESI-MS has been well-recognized for protein characterization since 1990s. However, the widespread adoption of cIEF-MS for the characterization of proteoforms had been impeded by several technical challenges, including the lack of highly sensitive and robust ESI interface for coupling cIEF to MS, ESI suppression of analytes from ampholytes, and the requirement of manual operations. In this mini review, we summarize the technical improvements of cIEF-ESI-MS for characterizing proteoforms and highlight some recent applications to hydrophobic proteins, urinary albumin variants, charge variants of monoclonal antibodies, and large-scale TDP of complex proteomes.

Automated Capillary Isoelectric Focusing-Tandem Mass Spectrometry for Qualitative and Quantitative Top-Down Proteomics

Top-down proteomics (TDP) aims to delineate proteomes in a proteoform-specific manner, which is vital for accurately understanding protein function in cellular processes. It requires high-capacity separation of proteoforms before mass spectrometry (MS) and tandem MS (MS/MS). Capillary isoelectric focusing (cIEF)-MS has been recognized as a useful tool for TDP in the 1990s because cIEF is capable of high-resolution separation of proteoforms. Previous cIEF-MS studies concentrated on measuring the protein's mass without MS/MS, impeding the confident proteoform identification in complex samples and the accurate localization of post-translational modifications on proteoforms. Herein, for the first time, we present automated cIEF-MS/MS-based TDP for large-scale delineation of proteoforms in complex proteomes. Single-shot cIEF-MS/MS identified 711 proteoforms from an Escherichia coli (E. coli) proteome consuming only nanograms of proteins. Coupling two-dimensional size-exclusion chromatography (SEC)-cIEF to ESI-MS/MS enabled the identification of nearly 2000 proteoforms from the E. coli proteome. Label-free quantitative TDP of zebrafish male and female brains using SEC-cIEF-MS/MS quantified thousands of proteoforms and revealed sex-dependent proteoform profiles in brains. Particularly, we discovered several proteolytic proteoforms of pro-opiomelanocortin and prodynorphin with significantly higher abundance in male zebrafish brains as potential endogenous hormone proteoforms. Multilevel quantitative proteomics (TDP and bottom-up proteomics) of the brains revealed that the majority of proteoforms having statistically significant difference in abundance between genders showed no abundance difference at the protein group level. This work represents the first multilevel quantitative proteomics study of sexual dimorphism of the brain.

Simplified capillary isoelectric focusing with chemical mobilization for intact protein analysis

We report a capillary isoelectric focusing system based on a sequential injection method for simplified chemical mobilization. This system was coupled to an ion trap mass spectrometer with an electrokinetically pumped nanoelectrospray interface. The nanoelectrospray emitter employed an acidic sheath electrolyte. To simplify focusing and mobilization, a plug of ammonium hydroxide was first injected into the capillary, followed by a section of mixed sample and ampholyte. During focusing, the NH₃ H₂ O section worked as catholyte. As focusing progressed, the NH₃ H₂ O section was titrated to lower pH by the acidic sheath electrolyte. Chemical mobilization started automatically once the ammonium hydroxide was consumed by the acidic sheath flow electrolyte, which then acted as the mobilization solution. In this report, the lengths of the NH₃ H₂ O section and sample were optimized. With a 1 m long capillary, a relative short plug of the NH₃ H₂ O section (3 cm) produced both fast migration and reasonable separation resolution. The simplified capillary isoelectric focusing mass spectrometry system produced base peak intensity relative standard deviation of 8.5% and migration time relative standard deviation ≤0.6% for myoglobin and cytochrome C in triplicate runs.

Online Capillary IsoElectric Focusing-ElectroSpray Ionization Mass Spectrometry (CIEF-ESI MS) in Glycerol-Water Media for the Separation and Characterization of Hydrophilic and Hydrophobic Proteins

Capillary isoelectric focusing (CIEF) is a high-resolution technique for the separation of ampholytes, such as proteins, according to their isoelectric point. CIEF coupled online with MS is regarded as a promising alternative to 2-D PAGE for fast proteome analysis with high-resolving capabilities and enhanced structural information without the drawbacks of conventional slab-gel electrophoresis. However, online coupling has been rarely described, as it presents some difficulties. A new methodology for the online coupling of CIEF with electrospray ionization mass spectrometry (ESI-MS) has been developed in glycerol-water media. This new integrated methodology provides a mean for the characterization of a large number of hydrophilic and hydrophobic proteins.

On-line capillary isoelectric focusing hyphenated to native electrospray ionization mass spectrometry for the characterization of interferon-γ and variants

The on-line hyphenation of Capillary IsoElectric Focusing (CIEF) with ElectroSpray Ionization Mass Spectrometry (ESI/MS) has been carried out in a non-denaturing detection mode at the CIEF-MS interface.

Screening of complicated matrixes with paper assisted ultrasonic spray ionization mass spectrometry

To analyze compounds in complicated matrixes using mass spectrometry, we describe a novel ambient ionization approach, termed paper assisted ultrasonic spray ionization (PAUSI). The ionization process is based on the ultrasonic vibration of the piezoelectric ceramic disk, on which the samples are placed. Porous materials are utilized to generate fine initial droplet, which could alleviate matrix effect during ionization process for complicated matrix. PAUSI was evaluated as an attractive tool to screen analytes from complicated matrixes, such as (1) bovine serum with NaCl 150 g/L, (2) viscous samples, and (3) biological fluid, without any sample preparation. Moreover, it provides great advantage in simplifying the mass spectrometry analysis process, and the ionization device is inexpensive and easy to operate.

On-line CE/ESI/MS interfacing: recent developments and applications in proteomics

After shining as the ultimate separation - sequencing technique used for the successful completion of the Human Genome Project, in the early 2000s CE experienced lowered popularity among separation scientists. The renewed interest in recent years relates to the separation needs, especially in proteomics, metabolomics, and glycomics, where CE complements liquid chromatography techniques. This interest is further boosted by the regulators requiring additional separation techniques for characterization of newly developed pharmaceuticals. This paper gives a short overview of recent developments in the on-line interfacing of CE separation techniques with electrospray ionization/mass spectrometric analysis. Both the instrumentation and selected CE/ESI/MS applications including analyses of peptides, proteins, and glycans are discussed with the stress on research published in the past 3 years. Techniques related to the proteomic and glycomic analyses such as sample preconcentration, on-line protein digestion, and analyte derivatization prior CE/ESI/MS analysis are also included.

Comparison of in-gel protein separation techniques commonly used for fractionation in mass spectrometry-based proteomic profiling

Fractionation of complex samples at the cellular, subcellular, protein, or peptide level is an indispensable strategy to improve the sensitivity in mass spectrometry-based proteomic profiling. This study revisits, evaluates, and compares the most common gel-based protein separation techniques i.e. 1D SDS-PAGE, 1D preparative SDS-PAGE, IEF-IPG, and 2D-PAGE in their performance as fractionation approaches in nano LC-ESI-MS/MS analysis of a mixture of protein standards and mitochondrial extracts isolated from rat liver. This work demonstrates that all the above techniques provide complementary protein identification results, but 1D SDS-PAGE and IEF-IPG had the highest number of identifications. The IEF-IPG technique resulted in the highest average number of detected peptides per protein. The 2D-PAGE was evaluated as a protein fractionation approach. This work shows that the recovery of proteins and resulting proteolytic digests is highly dependent on the total volume of the gel matrix. The performed comparison of the fractionation techniques demonstrates the potential of a combination of orthogonal 1D SDS-PAGE and IEF-IPG for the improved sensitivity of profiling without significant decrease in throughput.

Capillary electrophoresis-mass spectrometry for the analysis of intact proteins 2007-2010

CE coupled to MS has proven to be a powerful analytical tool for the characterization of intact proteins, as it combines the high separation efficiency of CE with the selectivity of MS. This review provides an overview of the development and application of CE-MS methods within the field of intact protein analysis as published between January 2007 and June 2010. Ongoing technological developments with respect to CE-MS interfacing, capillary coatings for CE-MS, coupling of CIEF with MS and chip-based CE-MS are treated. Furthermore, CE-MS of intact proteins involving ESI, MALDI and ICP ionization is outlined and overviews of the use of the various CE-MS methods are provided by tables. Representative examples illustrate the applicability of CE-MS for the characterization of proteins, including glycoproteins, biopharmaceuticals, protein-ligand complexes, biomarkers and dietary proteins. It is concluded that CE-MS is a valuable technique with high potential for intact protein analysis, providing useful information on protein identity and purity, including modifications and degradation products.