CE & CE/MS Troubleshooting Guide

Significance of the Topic

Capillary electrophoresis (CE) and its coupling with mass spectrometry (CE/MS) provide high‐resolution separations and sensitive analyte detection in pharmaceutical, biochemical, and environmental analysis. Ensuring stable electrical currents, clean capillaries, and reliable solvent delivery is critical to maintain reproducibility, minimize downtime, and achieve accurate results.

Objectives and Overview of the Troubleshooting Guide

This guide systematically addresses frequent operational issues encountered in CE and CE/MS systems. It outlines causes and practical solutions for unstable currents, baseline fluctuations, signal spikes, migration time shifts, and hardware maintenance. The goal is to help analysts identify root causes quickly and restore optimal performance.

Methodology and Sample Preparation

Proper preparation and daily maintenance are essential:

• Use pressure‐resistant, CE‐compatible vials and HPLC‐grade solvents filtered through 0.2–0.45 μm filters.
• Condition uncoated capillaries sequentially with methanol, sodium hydroxide, water, and running buffer.
• Replace background electrolyte (BGE) daily and flush capillaries with 0.1 M NaOH or phosphoric acid followed by water and buffer.
• Inspect vials, electrodes, sprayer needles, and capillary ends for damage or precipitation.
• Store bare and coated capillaries according to manufacturer instructions and perform regular system cleaning cycles.

Instrumentation Used

• Agilent 7100 Capillary Electrophoresis System
• Sheath‐flow CE/MS sprayer assembly
• Isocratic solvent pumps with online degassing
• Mass spectrometer inlet with electrospray ionization
• Diode array detector or UV detector for lamp output monitoring

Main Findings and Discussion

Key issues and remedies:

• Unstable or no current: caused by empty capillaries, wrong buffers, bubbles, or poor electrical contact. Solution: refill buffers, flush capillaries, adjust sprayer position, and increase sheath‐liquid flow.
• Baseline spikes and jumps: due to precipitates, salt buildup, or siphoning. Solution: filter solvents, degas buffers, clean or replace capillaries, level vials correctly.
• Current breaks during injection: liquid gaps from gas suction or field variation. Solution: time‐program nebulizing gas, adjust gas pressure and vial heights, use internal standards.
• Migration time shifts and peak tailing: from capillary surface changes, adsorption, or hydraulic siphoning. Solution: condition capillaries consistently, use buffer additives or coated capillaries, reduce nebulizing pressure.
• Poor reproducibility and background MS current: caused by ionization variability, dirty sprayer needles, or buffer evaporation. Solution: employ deuterated internal standards, clean all fluidic connections, seal vials, and replenish buffers.

Benefits and Practical Applications

Implementing these troubleshooting strategies enhances throughput by reducing instrument downtime and improving data quality. Laboratories gain confidence in quantitative analyses, support quality assurance/control protocols, and streamline workflows in pharmaceutical development, clinical diagnostics, and environmental monitoring.

Future Trends and Potential Applications

Emerging trends include predictive maintenance driven by real‐time instrument diagnostics, automated capillary conditioning routines, and machine‐learning algorithms for root‐cause analysis. Novel capillary coatings and microfluidic integration promise further resolution improvements and system robustness.

Conclusion

Effective troubleshooting in CE and CE/MS hinges on systematic maintenance, careful solvent management, and proactive inspection of key hardware components. Adopting these best practices ensures reliable separations, consistent mass spectrometric detection, and sustained laboratory productivity.

References

• High Performance Capillary Electrophoresis (primer, 5990-3777EN)
• CE/MS Principles and Practices (guidebook, 5994-0112EN)