Objective:

To evaluate the performance of capillary electrophoresis-mass spectrometry (CE-MS) across various laboratories for its potential use in top-down proteomics.

Approach:

• Study Design: An international benchmarking study was conducted across 12 laboratories to evaluate CE-MS performance using diverse setups and user experiences.
• Sample Selection: Commercially available protein mixes and intact protein cell lysates were used to minimize variability and enhance reproducibility.
• Communication Strategy: Regular update meetings were held to ensure project alignment and address issues promptly.

Key Findings:

• CE-MS shows exceptional separation efficiency and low sample consumption.
• Many barriers to CE-MS adoption have been reduced, including improved interfaces and stability.
• CE-MS can complement established LC-MS approaches in top-down proteomics.

Interpretation:

The study suggests that CE-MS has made significant progress in robustness and reproducibility, which may facilitate its broader use in top-down proteomics.

Limitations:

• The findings are based on specific CE-MS setups, which may not be applicable to all laboratory environments.
• Differences in user experience and laboratory conditions may influence the reproducibility of results.

Conclusion:

The benchmarking study serves as a reference for future CE-MS applications, promoting standardization and potential adoption in proteoform analysis.