Thermo Scientific Q Exactive hybrid quadrupole-Orbitrap mass spectrometers with ZipChip system

Importance of the topic

Capillary electrophoresis (CE) coupled with electrospray ionization mass spectrometry (ESI-MS) provides a rapid, sensitive, and high-resolution approach for detailed structural characterization of biopharmaceutical analytes. This technique addresses critical needs in antibody, antibody-drug conjugate (ADC), subunit, and peptide analysis essential for development, quality control, and regulatory compliance in the biopharma sector.

Study objectives and overview

This application note outlines a comprehensive CE/ESI-MS workflow integrating Thermo Scientific Q Exactive hybrid quadrupole-Orbitrap mass spectrometers (Plus, HF, HF-X) with the 908 Devices ZipChip microfluidic system and BioPharma Finder software. The platform is designed to characterize intact antibodies, ADCs, antibody subunits, and peptides with minimal sample consumption and high throughput.

Methodology and instrumentation

• ZipChip microfluidic CE separation: delivers fast separations (e.g., intact mAb variants in ≤3 min).
• Q Exactive hybrid quadrupole-Orbitrap MS (Plus, HF, HF-X) with BioPharma option: provides high-resolution accurate mass (HRAM) detection in HMR mode.
• BioPharma Finder software: supports sliding-window MS acquisition, Xtract deconvolution, and monoisotopic mass determination.

Main results and discussion

• Intact mAb analysis: rapid baseline separation of glycoforms and lysine-clipping variants with mass accuracies better than 10 ppm.
• ADC characterization: heterogenous trastuzumab emtansine DAR distribution determined in under 1 min from picogram to nanogram injections.
• mAb subunit profiling: IdeS digestion and reduction separate light chain, Fd′, and Fc/2 subunits with monoisotopic masses within 5 ppm of theoretical values.
• Peptide mapping: 10-minute CE-MS/MS run yields 98–100% sequence coverage of heavy and light chains from 1 ng input.

Benefits and practical applications

• Minimal sample consumption (pg–ng) and no extensive pre-treatment required.
• Accelerated workflows complement LC-MS for high-throughput screening, QA/QC, and detailed structural analysis.
• High sensitivity and resolution support precise glycoform, charge variant, and DAR determinations essential for regulatory filing.

Future trends and opportunities

Advances in microfluidic CE-MS and Orbitrap detection are driving deeper proteoform profiling, real-time process monitoring, and automated high-throughput analyses. Coupling these platforms with advanced data analytics and machine learning will further enhance detection of low-abundance species and streamline biopharmaceutical development and quality control.

Conclusion

The Thermo Scientific ZipChip CE/ESI-MS solution, when paired with Q Exactive Orbitrap mass spectrometers and BioPharma Finder software, delivers a robust, fast, and sensitive workflow for comprehensive biopharmaceutical characterization. This integrated platform meets evolving demands for high-resolution separations, accurate mass measurements, and streamlined data analysis in biotherapeutic research and production.