Accurate determination of peptide phosphorylation stoichiometry via automated diagonal capillary electrophoresis coupled with mass spectrometry: proof of principle

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.

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 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.

Selectivity enhancement in capillary electrophoresis by means of two-dimensional separation or dual detection concepts

For the identification and quantification of analytes in complex samples, highly selective analytical strategies are required. The selectivity of single separation techniques such as gas chromatography (GC), liquid chromatography (LC), or capillary electrophoresis (CE) with common detection principles can be enhanced by hyphenating orthogonal separation techniques but also by using complementary detection systems. In this review, two-dimensional systems containing CE in at least one dimension are reviewed, namely LC-CE or 2D CE systems. Particular attention is paid to the aspect of selectivity enhancement due to the orthogonality of the different separation mechanisms. As an alternative concept, dual detection approaches are reviewed using the common detectors of CE such as UV/VIS, laser-induced fluorescence, capacitively coupled contactless conductivity (C⁴D), electrochemical detection, and mass spectrometry. Special emphasis is given to dual detection systems implementing the highly flexible C⁴D as one detection component. Selectivity enhancement can be achieved in case of complementarity of the different detection techniques.

Coupling of CE-MS for protein and peptide analysis

The review is focused on the latest developments in the analysis of proteins and peptides by capillary electrophoresis techniques coupled to mass spectrometry. First, the methodology and instrumentation are overviewed. In this section, recent progress in capillary electrophoresis with mass spectrometry interfaces and capillary electrophoresis with matrix-assisted laser desorption/ionization is mentioned, as well as separation tasks. The second part is devoted to applications-mainly bottom-up and top-down proteomics. It is obvious that capillary electrophoresis with mass spectrometry methods are well suited for peptide and protein analysis (proteomic research) and it is described how these techniques are complementary and not competitive with the often used liquid chromatography with mass spectrometry methods.

CE-ESI-MS for bottom-up proteomics: Advances in separation, interfacing and applications

With the development of more sensitive hyphenation strategies for capillary electrophoresis-electrospray-mass spectrometry the technique has reemerged as technique with high separation power combined with high sensitivity in the analysis of peptides and protein digests. This review will discuss the newly developed hyphenation strategies for CE-ESI-MS and their application in bottom-up proteomics as well as the applications in the same time span, 2009 to present, using co-axial sheathliquid. Subsequently all separate aspects in the development of a CE-ESI-MS method for bottom-up proteomics shall be discussed, highlighting certain applications and discussing pros and cons of the various choices. The separation of peptides in a capillary electrophoresis system is discussed including the great potential for modeling of this migration of peptides due to the simple electrophoretic separation process. Furthermore, the technical aspects of method development are discussed, namely; background electrolyte choice, coating of the separation capillary and chosen loading method. Finally, conclusions and an outlook on future developments in the field of bottom-up proteomics by CE-ESI-MS will be provided.

Direct and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring

Defining intracellular protein concentration is critical in molecular systems biology. Although strategies for determining relative protein changes are available, defining robust absolute values in copies per cell has proven significantly more challenging. Here we present a reference data set quantifying over 1800 Saccharomyces cerevisiae proteins by direct means using protein-specific stable-isotope labeled internal standards and selected reaction monitoring (SRM) mass spectrometry, far exceeding any previous study. This was achieved by careful design of over 100 QconCAT recombinant proteins as standards, defining 1167 proteins in terms of copies per cell and upper limits on a further 668, with robust CVs routinely less than 20%. The selected reaction monitoring-derived proteome is compared with existing quantitative data sets, highlighting the disparities between methodologies. Coupled with a quantification of the transcriptome by RNA-seq taken from the same cells, these data support revised estimates of several fundamental molecular parameters: a total protein count of ∼100 million molecules-per-cell, a median of ∼1000 proteins-per-transcript, and a linear model of protein translation explaining 70% of the variance in translation rate. This work contributes a “gold-standard” reference yeast proteome (including 532 values based on high quality, dual peptide quantification) that can be widely used in systems models and for other comparative studies.

Coupling capillary zone electrophoresis with electron transfer dissociation and activated ion electron transfer dissociation for top-down proteomics

Top-down proteomics offers the potential for full protein characterization, but many challenges remain for this approach, including efficient protein separations and effective fragmentation of intact proteins. Capillary zone electrophoresis (CZE) has shown great potential for separation of intact proteins, especially for differentially modified proteoforms of the same gene product. To date, however, CZE has been used only with collision-based fragmentation methods. Here we report the first implementation of electron transfer dissociation (ETD) with online CZE separations for top-down proteomics, analyzing a mixture of four standard proteins and a complex protein mixture from the Mycobacterium marinum bacterial secretome. Using a multipurpose dissociation cell on an Orbitrap Elite system, we demonstrate that CZE is fully compatible with ETD as well as higher energy collisional dissociation (HCD), and that the two complementary fragmentation methods can be used in tandem on the electrophoretic time scale for improved protein characterization. Furthermore, we show that activated ion electron transfer dissociation (AI-ETD), a recently introduced method for enhanced ETD fragmentation, provides useful performance with CZE separations to greatly increase protein characterization. When combined with HCD, AI-ETD improved the protein sequence coverage by more than 200% for proteins from both standard and complex mixtures, highlighting the benefits electron-driven dissociation methods can add to CZE separations.

Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry for quantitative parallel reaction monitoring of peptide abundance and single-shot proteomic analysis of a human cell line

We coupled capillary zone electrophoresis (CZE) with an ultrasensitive electrokinetically pumped nanospray ionization source for tandem mass spectrometry (MS/MS) analysis of complex proteomes. We first used the system for the parallel reaction monitoring (PRM) analysis of angiotensin II spiked in 0.45mg/mL of bovine serum albumin (BSA) digest. A calibration curve was generated between the loading amount of angiotensin II and intensity of angiotensin II fragment ions. CZE-PRM generated a linear calibration curve across over 4.5 orders of magnitude dynamic range corresponding to angiotensin II loading amount from 2amole to 150fmole. The relative standard deviations (RSDs) of migration time were <4% and the RSDs of fragment ion intensity were ∼20% or less except 150fmole angiotensin II loading amount data (∼36% RSD). We further applied the system for the first bottom up proteomic analysis of a human cell line using CZE-MS/MS. We generated 283 protein identifications from a 1h long, single-shot CZE MS/MS analysis of the MCF7 breast cancer cell line digest, corresponding to ∼80ng loading amount. The MCF7 digest was fractionated using a C18 solid phase extraction column; single-shot analysis of a single fraction resulted in 468 protein identifications, which is by far the largest number of protein identifications reported for a mammalian proteomic sample using CZE.