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Roxana McCloskey

Why capillary electrophoresis still matters in modern biopharma

Jun 9, 2026 | Biopharma, Blogs, CE | 0 comments

Read time: 2 minutes

When molecules evolve, analytical certainty must keep up

Biopharma development has changed dramatically over the past decade. Molecules are larger, more complex, and more diverse than ever, from highly engineered proteins and conjugates to long RNAs and gene‑based therapies. As modalities evolve, so do the analytical questions teams must answer at every stage of development.

Yet one requirement has remained constant: the need for high‑quality separation data that you can trust.

Capillary electrophoresis (CE) continues to play a critical role in modern biopharma analytics because it delivers exactly that: high‑resolution, reproducible separations that help teams see what matters, early and clearly, even as molecules and workflows grow more complex.

Resolution is no longer a nice-to-have

In early development, analytical methods often need to answer open‑ended questions:

· Are closely related species truly resolved, or simply co‑migrating?

· Are low‑abundance impurities being masked?

· Are observed changes real or artifacts of the method?

As programs move into process development and comparability studies, those questions become even more consequential. Subtle differences in size, charge, or integrity can influence stability profiles, control strategies, and downstream risk.

When reproducible resolution is insufficient, gaps often appear later, and show up as rework, delayed decisions, or uncertainty during stage handoffs. CE platforms that offer robust, high‑resolution separations help prevent these scenarios by providing clearer insight from the start and supporting confident decision‑making across development stages.

A trusted foundation for evolving modalities

CE has long been established as a reliable analytical technique in regulated biopharma environments. This reliability has fueled an increase in scope for how CE is deployed as a development tool.

Modern CE workflows are increasingly applied across:

· Protein purity and heterogeneity assessments

· mRNA integrity and impurity profiling

· Multi‑attribute analysis in gene and cell therapy programs

This adaptability allows teams to maintain a consistent analytical foundation, even as pipelines diversify. Rather than reinventing workflows for each new modality, CE enables scientists to extend proven separation principles to emerging challenges, preserving confidence while remaining flexible.

Confidence across handoffs, not just data points

In biopharma, data rarely live in isolation. Analytical results inform development decisions, process changes, comparability discussions, and regulatory submissions. Each handoff increases the importance of reproducibility and defensibility.

CE supports this reality by delivering separations that are consistent over time, teams, and stages. From early feasibility studies through structured development and, when appropriate, regulated environments, CE remains a trusted foundation. This reliability helps ensure that insights generated early remain meaningful later, reducing friction as programs advance.

Why CE now?

As development timelines compress and molecular complexity increases, biopharma teams need analytical approaches that balance resolution, robustness, and adaptability without introducing unnecessary complexity.

CE remains relevant not because it is familiar, but because it continues to deliver clear, defensible separations that scale with scientific ambition. Built on a trusted foundation and expanded to meet modern demands, it helps scientists focus on what matters most: understanding their molecules and moving forward with confidence.

Want to learn more?

Explore how CE workflows support protein, mRNA, and cell and gene therapy analytics across modern biopharma development.

Read a blog >

Explore the BioPhase 8800 system >

Discover the applications that SCIEX CE offers solutions for >

Where does capillary electrophoresis fit across drug development?

Capillary electrophoresis (CE) is not confined to a single point in the drug development lifecycle. Its value comes from the ability to deliver high‑resolution, reproducible separations that remain relevant as analytical questions evolve, from early discovery through late‑stage development and lot release.

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Why middle‑down and subunit MS analyses powered by EAD are transforming biopharmaceutical characterization

As an analytical strategy, middle-down mass spectrometry (MS) workflows characterize biotherapeutic proteins by analyzing large, digested protein fragments or defined subunits, rather than fully intact proteins (top-down) or digested peptides (bottom-up). A middle-down strategy combines the strengths of top-down and bottom-up approaches by delivering high sequence coverage and structural specificity while maintaining relatively simple sample preparation. In practice, middle-down analysis enables accurate mass measurement, rapid sequence confirmation, and localization of key post-translational modifications (PTMs) on protein subunits that are directly relevant to product quality.

Posted by

Roxana McCloskey

Roxana has over 15 years of experience in sales and marketing roles in the MS community. As Senior Global Marketing Manager for protein therapeutics at SCIEX, she specializes in communicating innovations in MS and CE-based workflows to the biopharma community.

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