Single-cell omic molecular profiling using capillary electrophoresis-mass spectrometry

SPE-CZE-MS Quantifies Zeptomole Amounts of Phosphorylated Peptides

Capillary zone electrophoresis (CZE) is gaining attention in the field of single-cell proteomics for its ultralow-flow and high-resolution separation abilities. Even more sample-limited yet rich in biological information are phosphoproteomics experiments, as the phosphoproteome composes only a fraction of the whole cellular proteome. Rapid analysis, high sensitivity, and maximization of sample utilization are paramount for single-cell analysis. Some challenges of coupling CZE analysis with mass spectrometry analysis (MS) of complex mixtures include 1. sensitivity due to volume loading limitations of CZE and 2. incompatibility of MS duty cycles with electropherographic time scales. Here, we address these two challenges as applied to single-cell-equivalent phosphoproteomics experiments by interfacing a microchip-based CZE device integrated with a solid-phase-extraction (SPE) bed with the Orbitrap Astral mass spectrometer. Using 225 phosphorylated peptide standards and phosphorylated peptide-enriched mouse brain tissue, we investigate microchip-based SPE-CZE functionality, quantitative performance, and complementarity to nano-LC-MS (nLC-MS) analysis. We highlight unique SPE-CZE separation mechanisms that can empower fit-for-purpose applications in single-cell-equivalent phosphoproteomics.

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.

A robust polymetallic-coated sheathless interface with high acid and alkali resistance for coupling capillary electrophoresis with mass spectrometry

A robust interface for coupling capillary electrophoresis (CE) to mass spectrometry (MS) was critical to maintain high separation efficiency of CE while achieving high sensitivity of MS. Current interfaces often suffer from problems such as reproducibility and ruggedness. For this purpose, a new polymetallic-coated sheathless interface was developed for the coupling of CE with MS. The electrical contact of the interface was achieved by etching one end of the fused silica capillary into a tapered tip using hydrofluoric acid (HF) solution, and then depositing a thin layer of chromium followed by a layer of platinum on it via physical vapor deposition technique. The performance of the new sheathless interface was systematically evaluated for the effect of flow rate and electrospray ionization (ESI) voltage on MS signal intensity, as well as the sample loading volume on CE separation efficiency and repeatability by using peptide standards and tryptic digest of bovine serum albumin (BSA). The interface was capable of generating stable electrospray even at ultra-low flow rate of 12.2 nL/min. In addition, the acid and alkali resistance of the polymetallic-coated emitter was tested by immersing it into 1 M HCL and 1 M NaOH solution, respectively. The results showed that polymetallic coating was still intact even after continuous immersion in the alkaline solution for 8 days (192 h) and a longer period in the acidic solution, indicating its excellent chemical stability. All the experimental results indicated that the sheathless interface fabricated by the new method in this study was robust and stable, making it promising for both sensitive and robust CE-MS sample analysis.

Development and Validation of RoboCap, a Robotic Capillary Platform to Automate Capillary Electrophoresis Mass Spectrometry En Route to High-Throughput Single-Cell Proteomics

Current developments in single-cell mass spectrometry (MS) aim to deepen proteome coverage while enhancing analytical speed to study entire cell populations, one cell at a time. Custom-built microanalytical capillary electrophoresis (μCE) played a critical role in the foundation of discovery single-cell MS proteomics. However, requirements for manual operation, substantial expertise, and low measurement throughput have so far hindered μCE-based single-cell studies on large numbers of cells. Here, we design and construct a robotic capillary (RoboCap) platform that grants single-cell CE-MS with automation for proteomes limited to less than ∼100 nL. RoboCap remotely controls precision actuators to translate the sample to the fused silica separation capillary, using vials in this work. The platform is hermetically enclosed and actively pressurized to inject ∼1-250 nL of the sample into a CE separation capillary, with errors below ∼5% relative standard deviation (RSD). The platform and supporting equipment were operated and monitored remotely on a custom-written Virtual Instrument (LabView). Detection performance was validated empirically on ∼5-250 nL portions of the HeLa proteome digest using a trapped ion mobility mass spectrometer (timsTOF PRO). RoboCap improved CE-ESI sample utilization to ∼20% from ∼3% on the manual μCE, the closest reference technology. Proof-of-principle experiments found proteome identification and quantification to robustly return ∼1,800 proteins (∼13% RSD) from ∼20 ng of the HeLa proteome digest on this earlier-generation detector. RoboCap automates CE-MS for limited sample amounts, paving the way to electrophoresis-based high-throughput single-cell proteomics.

Mass spectrometry-intensive top-down proteomics: an update on technology advancements and biomedical applications

Proteoforms are all forms of protein molecules from the same gene because of variations at the DNA, RNA, and protein levels, e.g., alternative splicing and post-translational modifications (PTMs). Delineation of proteins in a proteoform-specific manner is crucial for understanding their biological functions. Mass spectrometry (MS)-intensive top-down proteomics (TDP) is promising for comprehensively characterizing intact proteoforms in complex biological systems. It has achieved substantial progress in technological development, including sample preparation, proteoform separations, MS instrumentation, and bioinformatics tools. In a single TDP study, thousands of proteoforms can be identified and quantified from a cell lysate. It has also been applied to various biomedical research to better our understanding of protein function in regulating cellular processes and to discover novel proteoform biomarkers of diseases for early diagnosis and therapeutic development. This review covers the most recent technological development and biomedical applications of MS-intensive TDP.

A microfluidic chip-based capillary zone electrophoresis-mass spectrometry method for measuring adenosine 5'-Triphosphate and its similar nucleotide analogues

BACKGROUND

Extracellular ATP is involved in disorders that cause inflammation of the airways and cough, thus limiting its release has therapeutic benefits. Standard luminescence-based ATP assays measure levels indirectly through enzyme degradation and do not provide a simultaneous readout for other nucleotide analogues. Conversely, mass spectrometry can provide direct ATP measurements, however, common RPLC and HILIC methods face issues because these molecules are unstable, metal-sensitive analytes which are often poorly retained. These difficulties have traditionally been overcome using passivation or ion-pairing chromatography, but these approaches can be problematic for LC systems. As a result, more effective analytical methods are needed.

RESULTS

Here, we introduce a new application that uses microfluidic chip-based capillary zone electrophoresis-mass spectrometry (μCZE-MS) to measure ATP and its analogues simultaneously in biofluids. The commercially available ZipChip Interface and a High-Resolution Bare-glass microchip (ZipChip, HRB, 908 Devices Inc.) coupled to a Thermo Scientific Tribrid Orbitrap, were successfully used to separate and detect various nucleotide standards, as well as ATP, ADP, AMP, and adenosine in plasma and BALF obtained from naïve Brown Norway rats. The findings demonstrate that this approach can rapidly and directly detect ATP and its related nucleotide analogues, while also highlighting the need to preserve these molecules in biofluids with chelators like EDTA. In addition, we demonstrate that this μCZE-MS method is also suitable for detecting a variety of metabolites, revealing additional potential future applications.

SIGNIFICANCE

This innovative μCZE-MS approach provides a robust new tool to directly measure ATP and other nucleotide analogues in biofluids. This can enable the study of eATP in human disease and potentially contribute to the creation of ATP-targeting therapies for airway illnesses.

A critical evaluation of ultrasensitive single-cell proteomics strategies

Success of mass spectrometry characterization of the proteome of single cells allows us to gain a greater understanding than afforded by transcriptomics alone but requires clear understanding of the tradeoffs between analytical throughput and precision. Recent advances in mass spectrometry acquisition techniques, including updated instrumentation and sample preparation, have improved the quality of peptide signals obtained from single cell data. However, much of the proteome remains uncharacterized, and higher throughput techniques often come at the expense of reduced sensitivity and coverage, which diminish the ability to measure proteoform heterogeneity, including splice variants and post-translational modifications, in single cell data analysis. Here, we assess the growing body of ultrasensitive single-cell approaches and their tradeoffs as researchers try to balance throughput and precision in their experiments.

The 15-min (Sub)Cellular Proteome

Single-cell mass spectrometry (MS) opens a proteomic window onto the inner workings of cells. Here, we report the discovery characterization of the subcellular proteome of single, identified embryonic cells in record speed and molecular coverage. We integrated subcellular capillary microsampling, fast capillary electrophoresis (CE), high-efficiency nano-flow electrospray ionization, and orbitrap tandem MS. In proof-of-principle tests, we found shorter separation times to hinder proteome detection using DDA, but not DIA. Within a 15-min effective separation window, CE data-independent acquisition (DIA) was able to identify 1,161 proteins from single HeLa-cell-equivalent (∼200 pg) proteome digests vs. 401 proteins by the reference data-dependent acquisition (DDA) on the same platform. The approach measured 1,242 proteins from subcellular niches in an identified cell in the live Xenopus laevis (frog) embryo, including many canonical components of organelles. CE-MS with DIA enables fast, sensitive, and deep profiling of the (sub)cellular proteome, expanding the bioanalytical toolbox of cell biology.

Authorship Contributions

P.N. and B.S. designed the study. L.R.P. collected the X. laevis cell aspirates. B.S. prepared and measured the samples. B.S. and P.N. analyzed the data and interpreted the results. P.N. and B.S. wrote the manuscript. All the authors commented on the manuscript.

Ultralow flow liquid chromatography and related approaches: A focus on recent bioanalytical applications

Ultralow flow LC employs ultra-narrow bore columns and mid-range pL/min to low nL/min flow rates (i.e., ≤20 nL/min). The separation columns that are used under these conditions are typically 2-30 μm in inner diameter. Ultralow flow LC systems allow for exceptionally high sensitivity and frequently high resolution. There has been an increasing interest in the analysis of scarce biological samples, for example, circulating tumor cells, extracellular vesicles, organelles, and single cells, and ultralow flow LC was efficiently applied to such samples. Hence, advances towards dedicated ultralow flow LC instrumentation, technical approaches, and higher throughput (e.g., tens-to-hundreds of single cells analyzed per day) were recently made. Here, we review the types of ultralow flow LC technology, followed by a discussion of selected representative ultralow flow LC applications, focusing on the progress made in bioanalysis of amount-limited samples during the last 10 years. We also discuss several recently reported high-sensitivity applications utilizing flow rates up to 100 nL/min, which are below commonly used nanoLC flow rates. Finally, we discuss the path forward for future developments of ultralow flow LC.