Capillary electrophoresis-tandem mass spectrometry as a highly selective tool for the compositional and site-specific assessment of multiple peptide-deamidation

Separation of intact proteins by capillary electrophoresis

This work introduces novel and universal workflows for the analysis of intact proteins by capillary electrophoresis and presents guidelines for the targeted selection of appropriate background electrolytes (BGEs) by consideration of the target proteins' isoelectric point (pI). The suitability of neutral dimethyl polysiloxane (PDMS) capillaries with dynamic coatings of cationic cetyltrimethylammonium bromide (CTAB) or anionic sodium dodecyl sulfate (SDS), and bare fused silica (BFS) capillaries were systematically evaluated for the analysis of histidine and seven model proteins in six BGEs with pH values between 3.0 and 9.6. Multiple capillary and BGE combinations were suitable for the analysis of all proteins with molecular weights ranging from 13.7-150 kDa, and pIs between 4.7 and 9.6. The CTAB-PDMS capillary was best suited for low pH BGEs, while the SDS-PDMS and BFS capillary were superior for high pH BGEs. These combinations consistently resulted in sharp peak shapes and rapid migration times. pH values of BGEs closer to the proteins' pI produced poorer peak shapes and decreased effective mobilities due to suppressed ionisation. Plots of mobility vs. pH crossed at approximately the pI of the protein in most cases. The workflow was applied to the analysis of caseins and whey proteins in milk for the separation of the seven most abundant proteins, including the isoforms of A1 and A2 β-casein and β-lactoglobulin A and B.

Separation Abilities of Capillary Electrophoresis Coupled with Ion Mobility Mass Spectrometry for the Discrete Detection of Sequence Isomeric Peptides

The separation and discrete detection of isomeric sequence peptides with similar properties are important tasks for analytical science. Three different peptide isomers of 12 amino-acid residues long, containing direct and reverse regions of the alanine-valine-proline-isoleucine (AVPI) motif, were partially separated and discretely detected from their mixture using two approaches. Capillary electrophoresis enabled the separation and optical detection of the peptide sequence isomers close to the baseline. The ability to separate these sequence isomers from the mixture and discretely identify them from mass spectra has also been demonstrated by ion-mobility tandem mass spectrometry. Moreover, for the first time, capillary electrophoresis and ion-mobility mass spectrometry connected online have shown their ability for a discrete detection of the multidirectional sequence isomers.

Polyelectrolyte Multilayers in Capillary Electrophoresis

Capillary electrophoresis (CE) has been proven to be a performant analytical method to analyze both small and macro molecules. Indeed, it is capable of separating compounds of the same nature according to differences in their charge to size ratios, particularly proteins, monoclonal antibodies and peptides. However, one of the major obstacles to reach high separation efficiency remains the adsorption of solutes on the capillary wall. Among the different coating approaches used to control and minimize solute adsorption, polyelectrolyte multilayers can be applied to CE as a versatile approach. These coatings are made up of alternating layers of polycations and polyanions, and may be used in acidic, neutral or basic conditions depending on the solutes to be analyzed. This Review provides an overview of Successive Multiple Ionic-polymer Layer (SMIL) coatings used in CE, looking at how different parameters induce variations on the electro-osmotic flow (EOF), separation efficiency and coating stability, as well as their promising applications in the biopharmaceutical field.

Assessment of Macro- and Microheterogeneity of Monoclonal Antibodies Using Capillary Zone Electrophoresis Hyphenated with Mass Spectrometry

This chapter focuses on the application of capillary zone electrophoresis hyphenated with mass spectrometry (CZE-MS) for the characterization of monoclonal antibodies (mAbs). mAbs are complex molecules comprising different glycoforms and many other posttranslational modifications. In addition to this inherent microheterogeneity, misassembling of antibodies can take place during production contributing to their macroheterogeneity. CZE-MS is a versatile and powerful technique which has demonstrated high potential for the assessment of both micro- and macroheterogeneity of mAbs. In this chapter, technical and practical considerations for the characterization of mAbs by CZE-MS are described. CE-MS interfacing, capillary coatings for the prevention of mAb adsorption, and sample preparation considerations are covered in detail. The assessment of the macro- and microheterogeneity is discussed and exemplified through three different approaches involving analysis of intact, enzymatically digested, and reduced antibodies. The examples also illustrate the use of two commercially available interfacing techniques (i.e., sheath liquid and sheathless) as well as different types of capillary coatings (positively charged and neutral coatings).

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.

Recent developments on production, purification and biological activity of marine peptides

Marine peptides are one of the richest sources of structurally diverse bioactive compounds and a considerable attention has been drawn towards their production and bioactivity. However, there is a paucity in consolidation of emerging trends encompassing both production techniques and biological application. Herein, we intend to review the recent advancements on different production, purification and identification technologies used for marine peptides along with presenting their potential health benefits. Bibliometric analysis revealed a growing number of scientific publications on marine peptides (268 documents per year) with both Asia (37.2%) and Europe (33.1%) being the major contributors. Extraction and purification by ultrafiltration and enzymatic hydrolysis, followed by identification by chromatographic techniques coupled with an appropriate detector could yield a high content of peptides with improved bioactivity. Moreover, the multifunctional health benefits exerted by marine peptides including anti-microbial, antioxidant, anti-hypertension, anti-diabetes and anti-cancer along with their structure-activity relationship were presented. The future perspective on marine peptide research should focus on finding improved separation and purification technologies with enhanced selectivity and resolution for obtaining more novel peptides with high yield and low cost. In addition, by employing encapsulation strategies such as nanoemulsion and nanoliposome, oral bioavailability and bioactivity of peptides can be greatly enhanced. Also, the potential health benefits that are demonstrated by in vitro and in vivo models should be validated by conducting human clinical trials for a technology transfer from bench to bedside.

Site-Specific N-Linked Glycosylation Analysis of Human Carcinoembryonic Antigen by Sheathless Capillary Electrophoresis-Tandem Mass Spectrometry

With 28 potential N-glycosylation sites, human carcinoembryonic antigen (CEA) bears an extreme amount of N-linked glycosylation, and approximately 60% of its molecular mass can be attributed to its carbohydrates. CEA is often overexpressed and released by many solid tumors, including colorectal carcinomas. CEA displays an impressive heterogeneity and variability in sugar content; however, site-specific distribution of carbohydrate structures has not been reported so far. The present study investigated CEA samples purified from human colon carcinoma and human liver metastases and enabled the characterization of 21 out of 28 potential N-glycosylation sites with respect to their occupancy. The coverage was achieved by a multienzymatic digestion approach with specific enzymes, such as trypsin, endoproteinase Glu-C, and the nonspecific enzyme, Pronase, followed by analysis using sheathless CE-MS/MS. In total, 893 different N-glycopeptides and 128 unique N-glycan compositions were identified. Overall, a great heterogeneity was found both within (micro) and in between (macro) individual N-glycosylation sites. Moreover, notable differences were found on certain N-glycosylation sites between primary adenocarcinoma and metastatic tumor in regard to branching, bisection, sialylation, and fucosylation. Those features, if further investigated in a targeted manner, may pave the way toward improved diagnostics and monitoring of colorectal cancer progression and recurrence. Raw mass spectrometric data and Skyline processed data files that support the findings of this study are available in the MassIVE repository with the identifier MSV000086774 [DOI: 10.25345/C5Z50X].

Recent progress in the analysis of protein deamidation using mass spectrometry

Deamidation is a nonenzymatic and spontaneous posttranslational modification (PTM) that introduces changes in both structure and charge of proteins, strongly associated with aging proteome instability and degenerative diseases. Deamidation is also a common PTM occurring in biopharmaceutical proteins, representing a major cause of degradation. Therefore, characterization of deamidation alongside its inter-related modifications, isomerization and racemization, is critically important to understand their roles in protein stability and diseases. Mass spectrometry (MS) has become an indispensable tool in site-specific identification of PTMs for proteomics and structural studies. In this review, we focus on the recent advances of MS analysis in protein deamidation. In particular, we provide an update on sample preparation, chromatographic separation, and MS technologies at multi-level scales, for accurate and reliable characterization of protein deamidation in both simple and complex biological samples, yielding important new insight on how deamidation together with isomerization and racemization occurs. These technological progresses will lead to a better understanding of how deamidation contributes to the pathology of aging and other degenerative diseases and the development of biopharmaceutical drugs.

Recent trends of capillary electrophoresis-mass spectrometry in proteomics research

Progress in proteomics research has led to a demand for powerful analytical tools with high separation efficiency and sensitivity for confident identification and quantification of proteins, posttranslational modifications, and protein complexes expressed in cells and tissues. This demand has significantly increased interest in capillary electrophoresis-mass spectrometry (CE-MS) in the past few years. This review provides highlights of recent advances in CE-MS for proteomics research, including a short introduction to top-down mass spectrometry and native mass spectrometry (native MS), as well as a detailed overview of CE methods. Both the potential and limitations of these methods for the analysis of proteins and peptides in synthetic and biological samples and the challenges of CE methods are discussed, along with perspectives about the future direction of CE-MS. @ 2019 Wiley Periodicals, Inc. Mass Spec Rev 00:1-16, 2019.

Recent advances in capillary electrophoresis-mass spectrometry: Instrumentation, methodology and applications

Capillary electrophoresis (CE) offers fast and high-resolution separation of charged analytes from small injection volumes. Coupled to mass spectrometry (MS), it represents a powerful analytical technique providing (exact) mass information and enables molecular characterization based on fragmentation. Although hyphenation of CE and MS is not straightforward, much emphasis has been placed on enabling efficient ionization and user-friendly coupling. Though several interfaces are now commercially available, research on more efficient and robust interfacing with nano-electrospray ionization (ESI), matrix-assisted laser desorption/ionization (MALDI) and inductively coupled plasma mass spectrometry (ICP) continues with considerable results. At the same time, CE-MS has been used in many fields, predominantly for the analysis of proteins, peptides and metabolites. This review belongs to a series of regularly published articles, summarizing 248 articles covering the time between June 2016 and May 2018. Latest developments on hyphenation of CE with MS as well as instrumental developments such as two-dimensional separation systems with MS detection are mentioned. Furthermore, applications of various CE-modes including capillary zone electrophoresis (CZE), nonaqueous capillary electrophoresis (NACE), capillary gel electrophoresis (CGE) and capillary isoelectric focusing (CIEF) coupled to MS in biological, pharmaceutical and environmental research are summarized.

Investigating capillary electrophoresis-mass spectrometry for the analysis of common post-translational modifications

Capillary electrophoresis coupled to mass spectrometry is a very efficient analytical method for the analysis of post-translational modifications because of its high separation efficiency and high detection sensitivity. Here we applied CE-MS using three differently coated separation capillaries for in-depth analysis of a set of 70 synthetic post-translationally modified peptides (including phosphorylation, acetylation, methylation, and nitration). We evaluated the results in terms of peptide detection and separation characteristics and found that the use of a neutrally coated capillary resulted in highest overall signal intensity of singly modified peptides. In contrast, the use of a bare-fused silica capillary was superior in the identification of multi-phosphorylated peptides (12 out of 15 were identified). Fast separations of approximately 12 min could be achieved using a positively coated capillary, however, at the cost of separation efficiency. A comparison to nanoLC-MS revealed that multi-phosphorylated peptides interact with the RP material very poorly so that these peptides were either washed out or elute as very broad peaks from the nano column which results in a reduced peptide identification rate (7 out of 15). Moreover, the methods applied were found to be very well suited for the analysis of the acetylated, nitrated and methylated peptides. All 36 synthetic peptides, which exhibit one of those modifications, could be identified regardless of the method applied. As a final step in this study and as a proof of principle, the phosphoproteome enriched from PC-12 pheochromocytoma cells was analyzed by CE-MS resulting in 5686 identified and 4088 quantified phosphopeptides. We compared the characterized analytes to those identified by a nanoLC-MS proteomics study and found that less than one third of the phosphopeptides were identical, which demonstrates the benefit by combining different approaches quite impressively.