Simplifying CE−MS Operation. 2. Interfacing Low-Flow Separation Techniques to Mass Spectrometry Using a Porous Tip

Compatibility of highly sulfated cyclodextrin with electrospray ionization at low nanoliter/minute flow rates and its application to capillary electrophoresis/electrospray ionization mass spectrometric analysis of cathinone derivatives and their optical isomers

RATIONALE

Sodium salts of cyclodextrins are commonly used in capillary electrophoresis/mass spectrometry (CE/MS) analysis of illicit drugs and their optical isomers. To avoid the suppression effect of cyclodextrins under electrospray ionization (ESI), the partial filling technique (PFT) is commonly utilized, which has a limited resolution. Low-flow nano-ESI has been shown to reduce the suppression effect of the salts. To test the compatibility of low-flow ESI with a background electrolyte (BGE) containing sodium salts of cyclodextrin, sheathless narrow capillary CE/MS with flow rates of low nanoliters/minute (nL/min) was applied to the separation and detection of cathinones and their positional and optical isomers for the first time.

METHODS

Low-flow sheathless CE/MS using a 20-µm-i.d. capillary in conjunction with a porous tip interface was used for the separation of cathinone derivatives and their optical isomers. Highly sulfated γ-cyclodextrin (HS-γ-CD) in conjunction with (+)-18-crown-6-tetracarboxylic acid ((+)-18-C-6-TCA) was used as the BGE and an ion trap mass spectrometer operating in full scan mode was utilized.

RESULTS

Utilizing low flow rate (~10 nL/min) sheathless CE/MS, the use of the sodium salt of HS-γ-CD as the BGE was compared with the same solution using PFT. The relative and absolute sensitivity of detection of cathinones were about the same, indicating that under low-flow sheathless CE/MS there was no significant suppression due to the existence of HS-γ-CD in the electrospray process. However, enhanced resolution of cathinone derivatives and their positional and optical isomers was observed when the solution of HS-γ-CD was used as the BGE. The enhanced resolution was because of the presence of the HS-γ-CD in the entire capillary during the analysis. The addition of 15 mM (+)-18-C-6-TCA to the BGE containing HS-γ-CD further enhanced the resolution resulting in separation of all cathinones and their positional and optical isomers.

CONCLUSIONS

A novel CE/MS technique has been introduced that combines low-flow sheathless CE/MS, with HS-γ-CD and 15 mM (+)-18-C-6-TCA as the BGE for separation of cathinone derivatives as well as their positional and optical isomers.

Plasma metabolic profiling after cortical spreading depression in a transgenic mouse model of hemiplegic migraine by capillary electrophoresis – mass spectrometry

Cortical spreading depression-induced brain metabolic changes have been captured in the plasma of a transgenic migraine mouse model using CE-MS.

In-line separation by capillary electrophoresis prior to analysis by top-down mass spectrometry enables sensitive characterization of protein complexes

Intact protein analysis via top-down mass spectrometry (MS) provides a bird’s eye view over the protein complexes and complex protein mixtures with the unique capability of characterizing protein variants, splice isoforms, and combinatorial post-translational modifications (PTMs). Here we applied capillary electrophoresis (CE) through a sheathless CE–electrospray ionization interface coupled to an LTQ Velos Orbitrap Elite mass spectrometer to analyze the Dam1 complex from Saccharomyces cerevisiae. We achieved a 100-fold increase in sensitivity compared to a reversed-phase liquid chromatography coupled MS analysis of recombinant Dam1 complex with a total loading of 2.5 ng (12 amol). N-terminal processing forms of individual subunits of the Dam1 complex were observed as well as their phosphorylation stoichiometry upon Mps1p kinase treatment.

Sheathless capillary electrophoresis-tandem mass spectrometry for top-down characterization of Pyrococcus furiosus proteins on a proteome scale

Intact protein analysis via top-down mass spectrometry (MS) provides the unique capability of fully characterizing protein isoforms and combinatorial post-translational modifications (PTMs) compared to the bottom-up MS approach. Front-end protein separation poses a challenge for analyzing complex mixtures of intact proteins on a proteomic scale. Here we applied capillary electrophoresis (CE) through a sheathless capillary electrophoresis-electrospray ionization (CESI) interface coupled to an Orbitrap Elite mass spectrometer to profile the proteome from Pyrococcus furiosus. CESI-top-down MS analysis of Pyrococcus furiosus cell lysate identified 134 proteins and 291 proteoforms with a total sample consumption of 270 ng in 120 min of total analysis time. Truncations and various PTMs were detected, including acetylation, disulfide bonds, oxidation, glycosylation, and hypusine. This is the largest scale analysis of intact proteins by CE-top-down MS to date.

Differential detection of Rhizoma coptidis by capillary electrophoresis electrospray ionization mass spectrometry with a nanospray interface

A lab prototype CE-nanospray-MS platform with a high sensitivity porous sprayer was successfully applied in differential identification of Rhizoma coptidis in this paper. To obtain a stable and reliable nanospray, detailed optimizations about emitter geometry, buffer composition, emitter position, and spray voltage, as well as emitter cleanliness were discussed. Results showed that the reproducibility and sensitivity for separations of alkaloid standards were satisfactory using CE-nanospray-MS, which were also compared to ultra-HPLC (UHPLC)-MS. Their signal responds were at the same order of magnitude (intensities: 0.8 - 1.5 × 10(8) vs. 3.8 - 6.2 × 10(8) ), even though a 2 nL injection for CE was 2500-fold lower than UHPLC (5 μL injection). The absolute LOD results of CE-MS showed a remarkable superiority (18-24 fg), equal to 1000-fold lower than that of UHPLC-MS. Principal component analysis (PCA) of adulterated R. coptidis showed that this protocol had the ability to profile and qualify complex herb medicines, which also created a great potential for evaluation and qualification of rare and valuable Chinese medicines in future.

Analysis of monoclonal antibody by a novel CE-UV/MALDI-MS interface

mAbs are highly complex proteins that present a wide range of microheterogeneity that requires multiple analytical methods for full structure assessment and quality control. As a consequence, the characterization of mAbs on different levels is particularly product- and time-consuming. CE-MS couplings, especially to MALDI, appear really attractive methods for the characterization of biological samples. In this work, we report the last instrumental development and performance of the first totally automated off-line CE-UV/MALDI-MS/MS. This interface is based on the removal of the original UV cell of the CE apparatus, modification of the spotting device geometry, and creation of an integrated delivery matrix system. The performance of the method was evaluated with separation of five intact proteins and a tryptic digest mixture of nine proteins. Intact protein application shows the acquisition of electropherograms with high resolution and high repeatability. In the peptide mapping approach, a total number of 154 unique identified peptides were characterized using MS/MS spectra corresponding to average sequence coverage of 64.1%. Comparison with NanoLC/MALDI-MS/MS showed complementarity at the peptide level with an increase of 42% when using CE/MALDI-MS coupling. Finally, this work represents the first analysis of intact mAb charge variants by CZE using an MS detection. Moreover, using a peptide mapping approach CE-UV/MALDI-MS/MS fragmentation allowed 100% sequence coverage of the light chain and 92% of the heavy chain, and the separation of four major glycosylated peptides and their structural characterization.

Capillary-electrophoresis mass spectrometry for the detection of carbapenemases in (multi-)drug-resistant Gram-negative bacteria

In a time in which the spread of multidrug resistant microorganisms is ever increasing, there is a need for fast and unequivocal identification of suspect organisms to supplement existing techniques in the clinical laboratory, especially in single bacterial colonies. Mass-spectrometry coupled with efficient peptide separation techniques offer great potential for identification of resistant-related proteins in complex microbiological samples in an unbiased manner. Here, we developed a capillary electrophoresis-electrospray ionization-tandem mass spectrometry CE-ESI-MS/MS bottom-up proteomics workflow for sensitive and specific peptide analysis with the emphasis on the identification of β-lactamases (carbapenemases OXA-48 and KPC in particular) in bacterial species. For this purpose, tryptic peptides from whole cell lysates were analyzed by sheathless CE-ESI-MS/MS and proteins were identified after searching of the spectral data against bacterial protein databases. The CE-ESI-MS/MS workflow was first evaluated using a recombinant TEM-1 β-lactamase, resulting in 68% of the amino acid sequence being covered by 20 different unique peptides. Subsequently, a resistant and susceptible Escherichia coli lab strain were analyzed and based on the observed β-lactamase peptides, the two strains could easily be discriminated. Finally, the method was tested in an unbiased setup using a collection of in-house characterized OXA-48 (n = 17) and KPC (n = 10) clinical isolates. The developed CE-ESI-MS/MS method was able to identify the presence of OXA-48 and KPC in all of the carbapenemase positive samples, independent of species and degree of susceptibility. Four negative controls were tested and classified as negative by this method. Furthermore, a number of extended-spectrum beta-lactamases (ESBL) were identified in the same analyses, confirming the multiresistant character in 19 out of 27 clinical isolates. Importantly, the method performed equally well on protein lysates from single colonies. As such, it demonstrates CE-ESI-MS/MS as a potential next generation mass spectrometry platform within the clinical microbiology laboratory.

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.

Recent advances in the analysis of therapeutic proteins by capillary and microchip electrophoresis

The development of therapeutic proteins and peptides is an expensive and time-intensive process. Biologics, which have become a multi-billion dollar industry, are chemically complex products that require constant observation during each stage of development and production. Post-translational modifications along with chemical and physical degradation from oxidation, deamidation, and aggregation, lead to high levels of heterogeneity that affect drug quality and efficacy. The various separation modes of capillary electrophoresis (CE) are commonly utilized to perform quality control and assess protein heterogeneity. This review attempts to highlight the most recent developments and applications of CE separation techniques for the characterization of protein and peptide therapeutics by focusing on papers accepted for publication in the in the two-year period between January 2012 and December 2013. The separation principles and technological advances of CE, capillary gel electrophoresis, capillary isoelectric focusing, capillary electrochromatography and CE-mass spectrometry are discussed, along with exciting new applications of these techniques to relevant pharmaceutical issues. Also included is a small selection of papers on microchip electrophoresis to show the direction this field is moving with regards to the development of inexpensive and portable analysis systems for on-site, high-throughput analysis.

Recent developments in liquid-phase separation techniques for metabolomics

Metabolomics is the comprehensive analysis of low molecular weight compounds in biological samples such as cells, body fluids and tissues. Comprehensive profiling of metabolites in complex sample matrices with the current analytical toolbox remains a huge challenge. Over the past few years, liquid chromatography–mass spectrometry (LC–MS) and capillary electrophoresis–mass spectrometry (CE–MS) have emerged as powerful complementary analytical techniques in the field of metabolomics. This Review provides an update of the most recent developments in LC–MS and CE–MS for metabolomics. Concerning LC–MS, attention is paid to developments in column technology and miniaturized systems, while strategies are discussed to improve the reproducibility and the concentration sensitivity of CE–MS for metabolomics studies. Novel interfacing techniques for coupling CE to MS are also considered. Representative examples illustrate the potential of the recent developments in LC–MS and CE–MS for metabolomics. Finally, some conclusions and perspectives are provided.

Capillary zone electrophoresis for analysis of complex proteomes using an electrokinetically pumped sheath flow nanospray interface

The vast majority of proteomic studies employ RP-HPLC coupled with MS/MS for analysis of the tryptic digest of a cellular lysate. This technology is quite mature, and typically provides identification of hundreds to thousands of peptides, which is used to infer the identity of hundreds to thousands of proteins. These studies usually require milligrams to micrograms of starting material. CZE provides an interesting alternative separation method based on a different separation mechanism than HPLC. CE received some attention for protein analysis beginning 25 years ago. Those efforts stalled because of the limited performance of the electrospray interfaces and the limited speed and sensitivity of mass spectrometers of that era. This review considers a new electrospray interface design coupled with Orbitrap Velos and linear Q-trap mass spectrometers. CZE coupled with this interface and these detectors provides single shot detection of >1250 peptides from an Escherichia coli digest in less than 1 h, identification of nearly 5000 peptides from analysis of seven fractions produced by SPE of the E. coli digest in a 6 h total analysis time, low attomole detection limits for peptides generated from standard proteins, and high zeptomole detection limits for selected ion monitoring of peptides. Incorporation of an integrated on-line immobilized trypsin microreactor allows digestion and analysis of picogram amounts of a complex eukaryotic proteome.

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

RATIONALE

This paper introduces a novel ultrafast capillary electrophoresis (UFCE) mass spectrometry (MS) method comprised of a short (< 20 cm) and narrow (≤ 5 µm) capillary, with an integrated porous segment at the terminus of the capillary, for sheathless interfacing of CE to MS. The sheathless nature of the interface minimizes dead volume which is particularly important for ultrafast CE because of the small diameters of the capillaries.

METHODS

The separation voltage across the capillary was set to produce an electric field of ≥1000 V/cm to provide an analysis time of approximately 1 min. For the analysis of peptides and protein digests, a background electrolyte containing 0.1% cationic polymer (polybrene or Poly-E) in 0.1% acetic acid in water was used to prevent analyte-wall interaction.

RESULTS

Uniquely, the porous tip of the capillary is adjustable. This allows the porous tip to be pulled inside the sheath liquid for sample stacking during injection, or sample focusing in isoelectric focusing (IEF), or, alternatively, pushed outside of the sheath liquid for electrospray ionization (ESI). The adjustable interface preserves electrical conductivity during electrokinetic injection with reverse electro-osmotic flow. Therefore, pre-concentration of analytes at the capillary inlet is achieved without the need to disassemble the interface, improving the throughput.

CONCLUSIONS

As a proof of concept, the application of UFCE-MS was demonstrated by the analysis of a peptide mixture and a protein digest in ~1 min.

Stable, reproducible, and automated capillary zone electrophoresis-tandem mass spectrometry system with an electrokinetically pumped sheath-flow nanospray interface

A PrinCE autosampler was coupled to a Q-Exactive mass spectrometer by an electrokinetically pumped sheath-flow nanospray interface to perform automated capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry (CZE-ESI-MS/MS). 20ng aliquots of an Escherichia coli digest were injected to evaluate the system. Eight sequential injections over an 8-h period identified 1115±70 (relative standard deviation, RSD=6%) peptides and 270±8 (RSD=3%) proteins per run. The average RSDs of migration time, peak intensity, and peak area were 3%, 24% and 19%, respectively, for 340 peptides with high intensity. This is the first report of an automated CZE-ESI-MS/MS system using the electrokinetically pumped sheath-flow nanospray interface. The results demonstrate that this system is capable of reproducibly identifying over 1000 peptides from an E. coli tryptic digest in a 1-h analysis time.

Low-picomolar analysis of peptides by on-line coupling of fritless solid-phase extraction to sheathless capillary electrophoresis-mass spectrometry

A novel fritless solid-phase extraction (SPE) microcartridge was designed for combination with sheathless capillary electrophoresis-mass spectrometry (sheathless CE-MS) employing a prototype porous-tip capillary for nanoelectrospray ionization (nanoESI). The inlet of the separation capillary (30μm inner diameter (id), 150μm outer diameter (od)) was inserted in a 4mm long SPE microcartridge (150μm id, 365μm od) packed with a C18 sorbent of 55-105μm particle size. Performance of the SPE-CE-MS system was evaluated using diluted solutions of the three opioid peptides dynorphin A (1-7) (DynA), endomorphin 1 (End1) and met-enkephalin (Met). Sample volumes of 1.5μL were loaded on the SPE microcartridge and the retained peptides were eluted with 22nL of an acidic methanol/water (60:40, v/v) solution. Using a pressure of 50mbar during separation to speed up the analysis, good peptide resolution was obtained with acceptable plate numbers (between 53,000 and 92,000). Intraday relative standard deviations (% RSD) for peptide migration times and peak areas were below 4% and 9%, respectively. The SPE-CE-MS method showed good linearity in the 0.05-5ngmL(-1) range and limits of detection (LODs) were 10pgmL(-1). However, loading a larger volume of sample (8μL), LODs could be decreased down to 2pgmL(-1) (2.2-3.5pM). This represents an improvement of up to 5000-fold with respect to the LODs achieved by sheathless CE-MS without on-line preconcentration demonstrating the potential of on-line SPE for further enhancing sensitivity.

Capillary zone electrophoresis-multiple reaction monitoring from 100 pg of RAW 264.7 cell lysate digest

Capillary zone electrophoresis-multiple/single reaction monitoring (CZE-MRM/SRM), which employed an electrokinetically driven sheath-flow electrospray interface, was used for the rapid and highly sensitive detection of protein analytes in complex tryptic digests. MRM channels were developed against a commercial exponential mixture of bovine proteins. Five proteins spanning four orders of magnitude concentration range were confidently detected from only 2.5 ng of the digest mixture; the mass detection limits (S/N = 3) of two detected proteins, alpha-casein and glutamate dehydrogenase were about 600 zmol and 30 amol, respectively. This technique was then applied to a RAW 264.7 cell lysate digest. Three proteins were confidently and reproducibly detected from 100 pg of this digest. The sample amount corresponds to the approximate protein content from a single cell, which suggests that CZE-MRM may be a useful analytical tool in chemical cytometry. In addition to providing highly sensitive detection of proteins in complex mixtures, this system is highly rapid; migration time of the protein digests was less than 10 min.

Recent advances in coupling capillary electrophoresis-based separation techniques to ESI and MALDI-MS

Coupling CE-based separation techniques to MS creates a powerful platform for analysis of a wide range of biomolecules from complex samples because it combines the high separation efficiency of CE and the sensitivity and selectivity of MS detection. ESI and MALDI, as the most common soft ionization techniques employed for CE and MS coupling, offer distinct advantages for biomolecular characterization. This review is focused primarily on technological advances in combining CE and chip-based CE with ESI and MALDI-MS detection in the past five years. Selected applications in the analyses of metabolites, peptides, and proteins with recently developed CE-MS platforms are also highlighted.

Dielectric barrier electrospray-polarity cycle and trigger

The parameters influencing the combination of the dielectric barrier electrospray (DB-ES) with an ion trap mass spectrometer are investigated. Two approaches are presented: the application of different polarity cycles in the DB electrospray high voltage signal and the triggering of it to an output signal received by the mass spectrometer. Both approaches are addressed to improve the detection sensitivity over the sensitivity of conventional nano ES.

Non-aqueous capillary electrophoresis for the analysis of acidic compounds using negative electrospray ionization mass spectrometry

Non-aqueous capillary electrophoresis (NACE) is an attractive CE mode, in which water solvent of the background electrolyte (BGE) is replaced by organic solvent or by a mixture of organic solvents. This substitution alters several parameters, such as the pKa, permittivity, viscosity, zeta potential, and conductivity, resulting in a modification of CE separation performance (i.e., selectivity and/or efficiency). In addition, the use of NACE is particularly well adapted to ESI-MS due to the high volatility of solvents and the low currents that are generated. Organic solvents reduce the number of side electrochemical reactions at the ESI tip, thereby allowing the stabilization of the ESI current and a decrease in background noise. All these features make NACE an interesting alternative to the aqueous capillary zone electrophoresis (CZE) mode, especially in combination with mass spectrometry (MS) detection. The aim of this work was to evaluate the use of NACE coupled to negative ESI-MS for the analysis of acidic compounds with two available CE-MS interfaces (sheath liquid and sheathless). First, NACE was compared to aqueous CZE for the analysis of several pharmaceutical acidic compounds (non-steroidal anti-inflammatory drugs, NSAIDs). Then, the separation performance and the sensitivity achieved by both interfaces were evaluated, as were the impact of the BGE and the sample composition. Finally, analyses of glucuronides in urine samples subjected to a minimal sample pre-treatment ("dilute-and-shoot") were performed by NACE-ESI-MS, and the matrix effect was evaluated. A 20- to 100-fold improvement in sensitivity was achieved using the NACE mode in combination with the sheathless interface and no matrix effect was observed regardless of the interfaces.

Dating human bone: is racemization dating species-specific?

Our recently developed dating technique based on the racemization rate of aspartic acid was applied to dating human bone, as well as that of other mammals, utilizing capillary electrophoresis mass spectrometry. First, several well-dated (mostly (14)C-dated and with strong archeological evidence) human bones ranging in age from 150 to ~10,000 years were used to develop a calibration curve for human bone. The D/L ratio of aspartic acid for these specimens ranged from 2.4% to ~10%, with a correlation coefficient of better than 0.99, indicating a strong linear relationship between the d/l ratio of aspartic acid and the age of the specimens. This calibration curve can now be used to date human archeological specimens of unknown age, up to ~10,000 years. However, when the technique was applied to well-dated mixed species of larger mammal bones such as bison, whale, llama, etc., the calibration curve showed a slower rate of racemization with a lower correlation (0.88). As additional large mammal bones with less certain age (i.e., using archeological evidence alone with no (14)C-dating) were dated the correlation coefficient decreased to 0.70. The correlation coefficient decreased further to 0.58 when the racemization data from all mammals (including human) were added to the calibration curve, indicating the importance of using well-dated, species-specific specimens for forming a calibration curve. This conclusion is consistent with our previously published calibration curve for a single species of silk (Bombyx mori), which followed the expected reversible first-order kinetics. These results support species specificity of amino acid racemization dating.

Ultrasensitive and fast bottom-up analysis of femtogram amounts of complex proteome digests

Femtogram proteomics: An ultrasensitive capillary zone electrophoresis-mass spectrometry system that is based on an improved nanospray interface has been developed. This system is used for the analysis of picogram to femtogram amounts of E. coli digests; for example, over 100 proteins were identified from 16 pg digests by tandem mass spectrometry. AMTs=accurate mass and time tags.

Separation and characterization of nitrated variants of the major birch pollen allergen by CZE-ESI-μTOF MS

A CZE-ESI-TOF MS method has been optimized for the separation and identification of nitrated variants of the major birch pollen allergen from Betula verrucosa, isoform 1a (Bet v 1a). In-house nitration of recombinant Bet v 1a was done by peroxynitrite. As a BGE, 10 mmol/L ammonium bicarbonate with pH 7.50 provided best resolution. Nebulizer gas pressure and sheath liquid flow rate of 0.4 bar and 6 μL/min, respectively, maintained CZE selectivity and constituted stable electrospray conditions. A sheath liquid composition of 75% v/v methanol with 0.1% v/v formic acid in ultrapure water resulted in highest signal intensities. Alternatively, methanol could be replaced by 50% v/v isopropanol. Two modified allergen products derived from reaction mixtures that contained different amounts of the nitration reagent were compared by the elaborated CZE-ESI-TOF MS method. Up to twelve different Bet v 1a variants with one- to sixfold nitration could be distinguished. Several allergen fractions of equivalent nitration grade were resolved. Their different migration times indicate site-specific nitration with concomitant differences in pI and maybe also in hydrodynamic radius. The method allows for a characterization of in-house nitrated allergen samples that are intended for testing the postulated enhanced allergenicity of nitrated Bet v 1a variants.

Capillary isotachophoresis-nanoelectrospray ionization-selected reaction monitoring MS via a novel sheathless interface for high sensitivity sample quantification

A novel sheathless capillary isotachophoresis (CITP/CZE)-mass spectrometry (MS) interface featuring a large inner diameter (i.d.) separation capillary, and a detachable small i.d. porous electrospray ionization (ESI) emitter was developed in this study to simultaneously achieve large sample loading capacity and stable nanoESI operation. Crucial operating parameters, including sample loading volume, flow rate, and separation window, were systematically investigated to attain optimum CITP/CZE separation efficiency and MS detection sensitivity. The performance of CITP/CZE-nanoESI-MS using the new sheathless interface was evaluated for its achievable low limit of quantification (LOQ) by analyzing targeted peptides, leu-enkephalin and angiotensin II, spiked in a BSA tryptic digest matrix at different concentrations. A linear dynamic range spanning 4.5 orders of magnitude and a 10 pM LOQ with measurement reproducibility of the CV < 22% were obtained experimentally for both targeted peptides, representing a 5-fold sensitivity improvement as compared to using the sheath liquid interface developed previously.1.

High sensitivity capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry for the rapid analysis of complex proteomes

The vast majority of bottom-up proteomic studies employ reversed-phase separation of tryptic digests coupled with electrospray ionization tandem mass spectrometry. These studies are remarkably successful for the analysis of samples containing micrograms of protein. However, liquid chromatography tends to perform poorly for samples containing nanogram amounts of protein, presumably due to loss of trace-level peptides within the chromatographic system. Capillary zone electrophoresis provides a much simpler flow system and would appear to be an attractive alternative to liquid chromatography for separation of small peptide samples before electrospray ionization and mass spectrometry detection. However, capillary zone electrophoresis has received very little attention as a tool for analysis of complex proteomes. In 2012, we reported the use of capillary zone electrophoresis for the analysis of the secretome of Mycobacterium marinum, a model system for tuberculosis. Roughly 400 peptides and over 100 proteins were identified from this medium-complexity proteome; this identification required analysis of a set of 11 fractions and occupied three hours of mass spectrometer time. We have recently employed an improved capillary zone electrophoresis system for the analysis of 100 ng of the Escherichia coli proteome and observed over 1300 peptides and nearly 350 proteins in a single separation. More interestingly, analysis of 1 ng of the E. coli proteome yielded over 600 peptide and 140 protein groups. This sample size approaches that of a large eukaryotic cell, suggesting that capillary zone electrophoresis may ultimately be a useful tool for chemical cytometry.

Novel sheathless CE-MS interface as an original and powerful infusion platform for nanoESI study: from intact proteins to high molecular mass noncovalent complexes

Development of nano-electrospray (nanoESI) sources allowed to increase significantly the sensitivity which is often lacking when studying biological noncovalent assemblies. However, the flow rate used to infuse the sample into the mass spectrometer cannot be precisely controlled with nanoESI and the robustness of the system could represent an issue. In this study, we have used a sheathless capillary electrophoresis-mass spectrometry (CESI) prototype as a nanoESI infusion device. The hydrodynamic mobilization of the capillary content was characterized and the ability of the system to generate a stable electrospray under controlled flow rate conditions ranging from 4 up to 900 nL/min was demonstrated. The effect of the infusing flow rate on the detection of an intact model protein analyzed under native conditions was investigated. Results demonstrated a significant increase in sensitivity of 46-fold and a signal-to-noise ratio improvement of nearly 5-fold when using an infusing flow rate from 456.9 down to 13.7 nL/min. The CESI prototype was further used to detect successfully the β ring homodimer in its native conformation. Obtained results were compared with those achieved with conventional ESI. Intensity signals were increased by a factor of 5, while sample consumption decreased 80 times. β ring complexed with the P14 peptide was also studied. Finally, the CESI interface was used to observe the quaternary structure of native hemocyanins from Carcinus maenas crabs; this high molecular complex coexisting under various degrees of complexation and resulting in masses ranging from 445 kDa to 1.34 MDa.

Fast top-down intact protein characterization with capillary zone electrophoresis-electrospray ionization tandem mass spectrometry

Capillary zone electrophoresis (CZE)-electrospray ionization tandem mass spectrometry (ESI-MS/MS) was applied for rapid top-down intact protein characterization. A mixture containing four model proteins (cytochrome c, myoglobin, bovine serum albumin (BSA), and β-casein) was used as the sample. The CZE-ESI-MS system was first evaluated with the mixture. The four model proteins and five impurities were baseline-separated within 12 min. The limits of detection [signal-to-noise ratio (S/N) = 3] of the four model proteins ranged from 20 (cytochrome c) to 800 amol (BSA). The relative standard deviations of migration time and intensity for the four model proteins were less than 3% and 30%, respectively, in quintuplicate runs. CZE-ESI-MS/MS was then applied for top-down characterization of the mixture. Three of the model proteins (all except BSA) and an impurity (bovine transthyretin) were confidently identified by database searching of the acquired tandem spectra from protein fragmentation. Modifications including phosphorylation, N-terminal acetylation, and heme group binding were identified.

Comparing and combining capillary electrophoresis electrospray ionization mass spectrometry and nano-liquid chromatography electrospray ionization mass spectrometry for the characterization of post-translationally modified histones

We present the first comprehensive capillary electrophoresis electrospray ionization mass spectrometry (CESI-MS) analysis of post-translational modifications derived from H1 and core histones. Using a capillary electrophoresis system equipped with a sheathless high-sensitivity porous sprayer and nano-liquid chromatography electrospray ionization mass spectrometry (nano-LC-ESI-MS) as two complementary techniques, we characterized H1 histones isolated from rat testis. Without any pre-separation of the perchloric acid extraction, a total of 70 different modified peptides, including 50 phosphopeptides, were identified in the rat linker histones H1.0, H1a-H1e, and H1t. Out of the 70 modified H1 histone peptides, 27 peptides could be identified with CESI-MS only, and 11 solely with LC-ESI-MS. Immobilized metal-affinity chromatography enrichment prior to MS analysis yielded a total of 55 phosphopeptides; 22 of these peptides could be identified only by CESI-MS, and 19 only by LC-ESI-MS, showing the complementarity of the two techniques. We mapped 42 H1 modification sites, including 31 phosphorylation sites, of which 8 were novel sites. For the analysis of core histones, we chose a different strategy. In a first step, the sulfuric-acid-extracted core histones were pre-separated using reverse-phase high-performance liquid chromatography. Individual rat testis core histone fractions obtained in this way were digested and analyzed via bottom-up CESI-MS. This approach yielded the identification of 42 different modification sites including acetylation (lysine and N(α)-terminal); mono-, di-, and trimethylation; and phosphorylation. When we applied CESI-MS for the analysis of intact core histone subtypes from butyrate-treated mouse tumor cells, we were able to rapidly detect their degree of modification, and we found this method very useful for the separation of isobaric trimethyl and acetyl modifications. Taken together, our results highlight the need for additional techniques for the comprehensive analysis of post-translational modifications. CESI-MS is a promising new proteomics tool as demonstrated by this, the first comprehensive analysis of histone modifications, using rat testis as an example.

Rapid and multi-level characterization of trastuzumab using sheathless capillary electrophoresis-tandem mass spectrometry

Monoclonal antibodies (mAbs) are highly complex proteins that display a wide range of microheterogeneity that requires multiple analytical methods for full structure assessment and quality control. As a consequence, the characterization of mAbs on different levels is particularly product - and time - consuming. This work presents the characterization of trastuzumab sequence using sheathless capillary electrophoresis (referred as CESI) – tandem mass spectrometry (CESI-MS/MS). Using this bottom-up proteomic-like approach, CESI-MS/MS provided 100% sequence coverage for both heavy and light chain via peptide fragment fingerprinting (PFF) identification. The result was accomplished in a single shot, corresponding to the analysis of 100 fmoles of digest. The same analysis also enabled precise characterization of the post-translational hot spots of trastuzumab, used as a representative widely marketed therapeutic mAb, including the structural confirmation of the five major N-glycoforms.

Integrated capillary zone electrophoresis-electrospray ionization tandem mass spectrometry system with an immobilized trypsin microreactor for online digestion and analysis of picogram amounts of RAW 264.7 cell lysate

A capillary zone electrophoresis (CZE) electrospray ionization (ESI) tandem mass spectrometry (MS/MS) system was integrated with an immobilized trypsin microreactor. The system was evaluated and then applied for online digestion and analysis of picogram loadings of RAW 264.7 cell lysate. Protein samples were dissolved in a buffer containing 50% (v/v) acetonitrile (ACN), and then directly loaded into the capillary for digestion, followed by CZE separation and MS/MS identification. The organic solvent (50% (v/v) ACN) assisted the immobilized trypsin digestion and simplified the protein sample preparation protocol. Neither protein reduction nor alkylation steps were employed, which minimized sample loss and contamination. The integrated CZE-ESI-MS/MS system generated confident identification of bovine serum albumin (BSA) with 19% sequence coverage and 14 peptide identifications (IDs) when 20 fmol was loaded. When only 1 fmol of BSA was injected, one BSA peptide was consistently detected. For the analysis of a standard protein mixture, the integrated system produced efficient protein digestion and confident identification for proteins with different molecular weights and isoelectric points when a low-femtomole amount was loaded for each protein. We further applied the system for triplicate analysis of a RAW 264.7 cell lysate; 2 ± 1 and 7 ± 2 protein groups were confidently identified from only 300 pg and 3 ng loadings, respectively. The 300 pg sample loading corresponds to the protein content of three RAW 264.7 cells. In addition to high-sensitivity analysis, the integrated CZE-ESI-MS/MS system produces good reproducibility in terms of peptide and protein IDs, peptide migration time, and peptide intensity.

The coating of smart pH-responsive polyelectrolyte brushes in capillary and its application in CE

A novel pH-responsive coating technique was developed and applied to CE successfully in this paper. The coating was formed by bonding mixed opposite charge poly(acrylic acid) and poly(2-vinylpyridine) randomly onto the inner wall of a silica capillary. The coating processes were first characterized by ellipsometry and atomic force microscopy at macroscale and microscale, respectively. Measurements of EOF were implemented to confirm the coating. Direction and velocity of EOF became controllable from negative to positive, showing a perfect sigmoidal curve as the coating net charges alternated by the pH of BGE. The control of the EOF makes it possible to analyze different kinds of small molecules, peptides, and proteins successfully in the same capillary. Results showed that the stability and reproducibility for separations of fluoroquinolone standards were satisfactory for more than a hundred separations. A series of basic and acidic protein standards were separated with admirable efficiency and minimal adsorption using both polarities. The separation of tryptic BSA digest showed that the prepared capillary has immense potential in analyzing a single sample with both acidic and basic separations, which achieved the expectation in proteomics study by CE-MS.

Single-shot proteomics using capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry with production of more than 1250 Escherichia coli peptide identifications in a 50 min separation

Capillary zone electrophoresis (CZE)-electrospray ionization-tandem mass spectrometry (ESI-MS/MS) was optimized and applied for analysis of 1-100 ng Escherichia coli protein digests in a single run (single-shot analysis). The system employed an electrokinetically pumped nanospray interface, a coated capillary, and stacking conditions for sample injection. More than 1 250 peptides were identified by optimized single-shot CZE-ESI-MS/MS with 100 ng digest loaded and 50 min analysis time. When 10 ng and 1 ng digests were loaded, about 1 000 and 600 peptides were identified in a single-shot analysis, respectively. Compared with single-shot ultraperformance liquid chromatography (UPLC)-ESI-MS/MS, CZE-ESI-MS/MS produced fewer peptide IDs (1 377 ± 128 vs 1 875 ± 32) for large sample loading amounts (100 ng) with the same mass spectrometer time (50 min). However, when the loaded digest was mass limited (1 ng), CZE-ESI-MS/MS generated many more peptide identifications than UPLC-ESI-MS/MS (627 ± 38 vs 342 ± 113). In addition, CZE-ESI-MS/MS and UPLC-ESI -MS/MS provided complementary peptide level identifications. These results suggest that CZE-ESI-MS/MS may be useful for large-scale, comprehensive, and confident proteomics analysis.

High-throughput capillary electrophoresis-mass spectrometry: from analysis of amino acids to analysis of protein complexes

Recent advances in capillary electrophoresis-mass spectrometry (CE-MS) interfacing using porous tip is leading to commercialization of CE-MS with a sheathless interface for the first time. The new sheathless interface in conjunction with CE capillary coatings using self-coating background electrolytes (BGE) has significantly simplified CE-MS analysis of complex mixtures. CE-MS, with its high separation efficiency, compound identification capability, and ability to rapidly separate compounds with a wide range of mass and charge while consuming only nanoliters of samples, has become a valuable analytical technique for the analysis of complex biological mixtures. These advances have allowed a single capillary to analyze a range of compounds including amino acids, their D/L enantiomers, protein digests, intact proteins, and protein complexes. With these capabilities, CE-MS is poised to become the multipurpose tool of separation scientists. More recently, an eight-capillary CE in conjunction with an 8-inlet mass spectrometry has allowed 8 CE-MS analyses to be performed concurrently, significantly increasing throughput.