Ultrafast capillary electrophoresis/mass spectrometry with adjustable porous tip for a rapid analysis of protein digest in about a minute

Data-Independent Acquisition Shortens the Analytical Window of Single-Cell Proteomics to Fifteen Minutes in Capillary Electrophoresis Mass Spectrometry

Separation in single-cell mass spectrometry (MS) improves molecular coverage and quantification; however, it also elongates measurements, thus limiting analytical throughput to study large populations of cells. Here, we advance the speed of bottom-up proteomics by capillary electrophoresis (CE) high-resolution mass spectrometry (MS) for single-cell proteomics. We adjust the applied electrophoresis potential to readily control the duration of electrophoresis. On the HeLa proteome standard, shorter separation times curbed proteome detection using data-dependent acquisition (DDA) but not data-independent acquisition (DIA) on an Orbitrap analyzer. This DIA method identified 1161 proteins vs 401 proteins by the reference DDA within a 15 min effective separation from single HeLa-cell-equivalent (∼200 pg) proteome digests. Label-free quantification found these exclusively DIA-identified proteins in the lower domain of the concentration range, revealing sensitivity improvement. The approach also significantly advanced the reproducibility of quantification, where ∼76% of the DIA-quantified proteins had <20% coefficient of variation vs ∼43% by DDA. As a proof of principle, the method allowed us to quantify 1242 proteins in subcellular niches in a single, neural-tissue fated cell in the live Xenopus laevis (frog) embryo, including many canonical components of organelles. DIA integration enhanced throughput by ∼2-4 fold and sensitivity by a factor of ∼3 in single-cell (subcellular) CE-MS proteomics.

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.

Capillary zone electrophoresis-mass spectrometry for top-down proteomics

Mass spectrometry (MS)-based top-down proteomics characterizes complex proteomes at the intact proteoform level and provides an accurate picture of protein isoforms and protein post-translational modifications in the cell. The progress of top-down proteomics requires novel analytical tools with high peak capacity for proteoform separation and high sensitivity for proteoform detection. The requirements have made capillary zone electrophoresis (CZE)-MS an attractive approach for advancing large-scale top-down proteomics. CZE has achieved a peak capacity of 300 for separation of complex proteoform mixtures. CZE-MS has shown drastically better sensitivity than commonly used reversed-phase liquid chromatography (RPLC)-MS for proteoform detection. The advanced CZE-MS identified 6,000 proteoforms of nearly 1,000 proteoform families from a complex proteome sample, which represents one of the largest top-down proteomic datasets so far. In this review, we focus on the recent progress in CZE-MS-based top-down proteomics and provide our perspectives about its future directions.

Toward Confirmatory On-Site Real-Time Detection of Emerging Drugs Using Portable Ultrafast Capillary Electrophoresis Mass Spectrometry

Currently, law enforcement agencies rely upon presumptive tests such as color tests (or spot tests) for on-site, real-time identification of forensic evidence, such as controlled substances. These tests are simple and easy to use and require no instrumentation. However, they are unreliable and have a large false positive rate. On the other hand, confirmatory tests are done in analytical laboratories using sophisticated instrumentation by expert analysts, and have lower false positive rates. However, they are bulky and impractical for on-site real-time analysis. To provide more accurate identification of forensic evidence on-site, in real-time, it is important to develop portable confirmatory instrumentation using information-rich technologies. Moreover, because the analysis of controlled substances could be complicated by the existence of various isomers (including optical isomers) it is desirable that the portable instruments have the capability to separate structural and optical isomers of the controlled substances, because scheduling is some times dependent upon which isomer is present. To this end, we have developed a portable ultrafast capillary electrophoresis (UFCE) system for the separation of controlled substances and their structural and optical isomers. The UFCE instrument has an integrated porous tip for facile interfacing with electrospray ionization mass spectrometry. The technique has been successfully applied to the analysis of mixtures of several controlled substances such as amphetamines, cathinones, nor-mephedrone, and pregabalin and their optical isomers in about a minute.

Microprobe Capillary Electrophoresis Mass Spectrometry for Single-cell Metabolomics in Live Frog (Xenopus laevis) Embryos

The quantification of small molecules in single cells raises new potentials for better understanding the basic processes that underlie embryonic development. To enable single-cell investigations directly in live embryos, new analytical approaches are needed, particularly those that are sensitive, selective, quantitative, robust, and scalable to different cell sizes. Here, we present a protocol that enables the in situ analysis of metabolism in single cells in freely developing embryos of the South African clawed frog (Xenopus laevis), a powerful model in cell and developmental biology. This approach uses a capillary microprobe to aspirate a defined portion from single identified cells in the embryo, leaving neighboring cells intact for subsequent analysis. The collected cell content is analyzed by a microscale capillary electrophoresis electrospray ionization (CE-ESI) interface coupled to a high-resolution tandem mass spectrometer. This approach is scalable to various cell sizes and compatible with the complex three-dimensional structure of the developing embryo. As an example, we demonstrate that microprobe single-cell CE-ESI-MS enables the elucidation of metabolic cell heterogeneity that unfolds as a progenitor cell gives rise to descendants during development of the embryo. Besides cell and developmental biology, the single-cell analysis protocols described here are amenable to other cell sizes, cell types, or animal models.

Optimization of mass spectrometric parameters improve the identification performance of capillary zone electrophoresis for single-shot bottom-up proteomics analysis

The effects of MS1 injection time, MS2 injection time, dynamic exclusion time, intensity threshold, and isolation width were investigated on the numbers of peptide and protein identifications for single-shot bottom-up proteomics analysis using CZE-MS/MS analysis of a Xenopus laevis tryptic digest. An electrokinetically pumped nanospray interface was used to couple a linear-polyacrylamide coated capillary to a Q Exactive HF mass spectrometer. A sensitive method that used a 1.4 Th isolation width, 60,000 MS2 resolution, 110 ms MS2 injection time, and a top 7 fragmentation produced the largest number of identifications when the CZE loading amount was less than 100 ng. A programmable autogain control method (pAGC) that used a 1.4 Th isolation width, 15,000 MS2 resolution, 110 ms MS2 injection time, and top 10 fragmentation produced the largest number of identifications for CZE loading amounts greater than 100 ng; 7218 unique peptides and 1653 protein groups were identified from 200 ng by using the pAGC method. The effect of mass spectrometer conditions on the performance of UPLC-MS/MS was also investigated. A fast method that used a 1.4 Th isolation width, 30,000 MS2 resolution, 45 ms MS2 injection time, and top 12 fragmentation produced the largest number of identifications for 200 ng UPLC loading amount (6025 unique peptides and 1501 protein groups). This is the first report where the identification number for CZE surpasses that of the UPLC at the 200 ng loading level. However, more peptides (11476) and protein groups (2378) were identified by using UPLC-MS/MS when the sample loading amount was increased to 2 μg with the fast method. To exploit the fast scan speed of the Q-Exactive HF mass spectrometer, higher sample loading amounts are required for single-shot bottom-up proteomics analysis using CZE-MS/MS.

Binding States of Protein-Metal Complexes in Cells

The identification of endogenous proteins as well as their binding to metal ions in living cells is determined by combining pulsed electrophoretic separations with nanoelectrospray ionization followed by mass spectrometric detection. This approach avoids problems resulting from the complicated cellular environment. In this manner, we demonstrate the rapid identification (300 ms or less) of intact proteins from living E. coli cells including the complexation of calmodulin with calcium ion. The latter showed different binding states from those observed in in vitro studies. These observations also reveal in vitro measurements do not necessarily represent the actual situation in living cells. We conclude that the attempted in situ measurement of intracellular proteins with minimal sampling processes should be preferred.

Ultrafast capillary electrophoresis/mass spectrometry of controlled substances with optical isomer separation in about a minute

RATIONALE

Analysis of forensic evidence by information-rich technologies such as mass spectrometry (MS) is one of the fastest growing areas in forensic analysis. To provide more accurate identification of forensic evidence, in the past few years there has been a growing interest in moving this technology to the field for on-site, real-time analysis. To this end, several portable mass spectrometers have been introduced; however, the analysis of controlled substances could be complicated by the existence of various isomers including optical isomers in which sentencing may depend on the identification of the isomer. To date very few portable separation devices are capable of separating and identifying the optical isomers.

METHODS

In this study, the application of the portable ultrafast capillary electrophoresis (UFCE) to the separation of controlled substances is presented and the results are compared with the results obtained from a bench-top CE system. Both a nominal mass ion trap mass spectrometer and an accurate mass orbitrap mass spectrometer were interfaced with CE using a porous tip capillary.

RESULTS

A mixture of several controlled substances can be separated and detected using UFCE/MS in about a minute using field strengths of ≥1000 V/cm. Furthermore, separation and detection of underivatized optical isomers of amphetamine, cathinone, nor-mephedrone, and pregabalin using UFCE/MS can be achieved with an analysis time of less than two minutes. Resolutions of 1.3, 3.7 and 3.8 were achieved for pregabalin, cathinone and nor-mephedrone, respectively, under UFCE/MS conditions.

CONCLUSIONS

Amphetamine, cathinone, nor-mephedrone and pregabalin were separated and detected in about a minute, demonstrating the utility of the portable CE instrument for the analysis of controlled substances and their optical isomers. Copyright © 2016 John Wiley & Sons, Ltd.

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.

Portable, Battery Operated Capillary Electrophoresis with Optical Isomer Resolution Integrated with Ionization Source for Mass Spectrometry

We introduce a battery operated capillary electrophoresis electrospray ionization (CE/ESI) source for mass spectrometry with optical isomer separation capability. The source fits in front of low or high resolution mass spectrometers similar to a nanospray source with about the same weight and size. The source has two high voltage power supplies (±25 kV HVPS) capable of operating in forward or reverse polarity modes and powered by a 12 V rechargeable lithium ion battery with operation time of ~10 h. In ultrafast CE mode, in which short narrow capillaries (≤15 μm i.d., 15-25 cm long) and field gradients ≥1000 V/cm are used, peak widths at the base are <1 s wide. Under these conditions, the source provides high resolution separation, including optical isomer resolution in ~1 min. Using a low resolution mass spectrometer (LTQ Velos) with a scan time of 0.07 s/scan, baseline separation of amino acids and their optical isomers were achieved in ~1 min. Moreover, bovine serum albumin (BSA) was analyzed in ~1 min with 56% coverage using the data-dependent MS/MS. Using a high resolution mass spectrometer (Thermo Orbitrap Elite) with 15,000 resolution, the fastest scan time achieved was 0.15 s, which was adequate for CE-MS analysis when optical isomer separation is not required or when the optical isomers were well separated. Figures of merit including a detection limit of 2 fmol and linear dynamic range of two orders of magnitude were achieved for amino acids.

Detachable strong cation exchange monolith, integrated with capillary zone electrophoresis and coupled with pH gradient elution, produces improved sensitivity and numbers of peptide identifications during bottom-up analysis of complex proteomes

A detachable sulfonate-silica hybrid strong cation-exchange monolith was synthesized in a fused silica capillary, and used for solid phase extraction with online pH gradient elution during capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS) proteomic analysis. Tryptic digests were prepared in 50 mM formic acid and loaded onto the strong cation-exchange monolith. Fractions were eluted using a series of buffers with lower concentration but higher pH values than the 50 mM formic acid background electrolyte. This combination of elution and background electrolytes results in both sample stacking and formation of a dynamic pH junction and allows use of relatively large elution buffer volumes while maintaining reasonable peak efficiency and resolution. A series of five pH bumps were applied to elute E. coli tryptic peptides from the monolith, followed by analysis using CZE coupled to an LTQ-Orbitrap Velos mass spectrometer; 799 protein groups and 3381 peptides were identified from 50 ng of the digest in a 2.5 h analysis, which approaches the identification rate for this organism that was obtained with an Orbitrap Fusion. We attribute the improved numbers of peptide and protein identifications to the efficient fractionation by the online pH gradient elution, which decreased the complexity of the sample in each elution step and improved the signal intensity of low abundance peptides. We also performed a comparative analysis using a nanoACQUITY UltraPerformance LCH system. Similar numbers of protein and peptide identifications were produced by the two methods. Protein identifications showed significant overlap between the two methods, whereas peptide identifications were complementary.

High speed capillary zone electrophoresis-mass spectrometry via an electrokinetically pumped sheath flow interface for rapid analysis of amino acids and a protein digest

While capillary zone electrophoresis (CZE) has been used to produce very rapid and efficient separations, coupling these high-speed separations with mass spectrometry (MS) has been challenging. Now, with much faster and sensitive mass spectrometers, it is possible to take full advantage of the CZE speed and reconstruct the fast migrating peaks. Here are three high-speed CZE-MS analyses via an electrokinetically pumped sheath-flow interface. The first separation demonstrates CZE-ESI-MS of an amino acid mixture with a 2-min separation, >50,000 theoretical plates, low micromolar concentration detection limits, and subfemtomole mass detection limits (LTQ XL mass spectrometer). The second separation with our recently improved third-generation CE-MS interface illustrates a 20 amino acid separation in ∼7min with an average over 200,000 plate counts, and results in almost-baseline resolution of structural isomers, leucine and isoleucine. The third separation is of a BSA digest with a reproducible CZE separation and mass spectrometry detection in 2min. CZE-MS/MS analysis of the BSA digest identified 31 peptides, produced 52% sequence coverage, and generated a peak capacity of ∼40 across the 1-min separation window (Q-Exactive mass spectrometer).

Two-dimensional separation of ionic species by hyphenation of capillary ion chromatography × capillary electrophoresis-mass spectrometry

The separation of complex mixtures such as biological or environmental samples requires high peak capacities, which cannot be established with a single separation technique. Therefore, multidimensional systems are in demand. In this work, we present the hyphenation of the two most important (orthogonal) techniques in ion analysis, namely, ion chromatography (IC) and capillary electrophoresis (CE), in combination with mass spectrometry. A modulator was developed ensuring a well-controlled coupling of IC and CE separations. Proof-of-concept measurements were performed using a model system consisting of nucleotides and cyclic nucleotides. The data are presented in a multidimensional contour plot. Analyte stacking in the CE separation could be exploited on the basis of the fact that the suppressed IC effluent is pure water.

Rapid analyses of proteomes and interactomes using an integrated solid-phase extraction-liquid chromatography-MS/MS system

Here, we explore applications of a LC system using disposable solid-phase extraction (SPE) cartridges and very short LC-MS/MS gradients that allows for rapid analyses in less than 10 min analysis time. The setup consists of an autosampler harboring two sets of 96 STAGE tips that function as precolumns and a short RP analytical column running 6.5 min gradients. This system combines efficiently with several proteomics workflows such as offline prefractionation methods, including 1D gel electrophoresis and strong-cation exchange chromatography. It also enables the analysis of interactomes obtained by affinity purification with an analysis time of approximately 1 h. In a typical shotgun proteomics experiment involving 36 SCX fractions of an AspN digested cell lysate, we detected over 3600 protein groups with an analysis time of less than 5.5 h. This innovative fast LC system reduces proteome analysis time while maintaining sufficient proteomic detail. This has particular relevance for the use of proteomics within a clinical environment, where large sample numbers and fast turnover times are essential.