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Roxana McCloskey

Where does capillary electrophoresis fit across drug development?

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

Read time: 4 minutes

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.

Rather than being replaced as programs progress, CE workflows are often adapted and refined, allowing teams to build on familiar data and methods instead of starting over at each stage.

Early development and feasibility: Answering open‑ended questions

In early research and feasibility studies, analytical methods are often exploratory. Molecules, or program direction, may still be changing, and scientists need visibility into unknown or poorly understood attributes.

At this stage, CE is used to:

· Rapidly assess size‑ or charge‑based profiles

· Identify fragmentation, heterogeneity, or integrity issues early

· Screen candidates or conditions with confidence in separation quality

The emphasis is on seeing what’s there, rather than meeting fixed specifications. Quick, high‑resolution separations help avoid false assumptions that can carry over into development.

Analytical and process development: Comparing, optimizing, and understanding change

As programs move into analytical and process development, the role of CE shifts from exploration to comparison. Scientists are focused on asking how and why they are seeing what they are, and if they are different than expectations, why those differences occur.

In this stage, CE is commonly used to:

· Compare lots, conditions, and process changes

· Monitor trends in purity, integrity, or heterogeneity

· Generate data that supports comparability and process optimization

Because CE methods can be tuned for either throughput or resolution, teams can balance speed with data depth as development needs evolve without abandoning the analytical approach they’ve already built.

Late‑stage development and preparation for QC transfer: Building confidence with defensible data

As development progresses toward late‑stage studies, expectations around reproducibility, robustness, and consistency increase. Analytical results must now support external decision‑making, including regulatory discussions and internal handoffs.

At this stage, CE supports:

· High‑confidence characterization for comparability and stability studies

· Robust, reproducible data across time and analysts

· Continuity of analytical understanding from earlier phases

The value of CE lies in data continuity, enabling teams to reference trends and insights established earlier, rather than re‑interpreting results from entirely different methods.

How this strengthens the lifecycle role of CE: One technique, multiple stages, without reinvention

Across all stages, the common theme is not that CE is “early‑stage” or “late‑stage,” but that it provides a stable analytical foundation that adapts as questions become more specific.

By supporting exploratory insight early, structured comparison in development, and defensible confidence later, CE helps biopharma teams reduce analytical friction across the lifecycle even as modalities, timelines, and expectations change.

Why SCIEX CE

CE is used across multiple stages of drug development, not as a single‑purpose analytical technique, but as a platform that adapts as analytical questions change.

Why SCIEX CE is well suited for modern drug development workflows

SCIEX CE solutions are designed to support analytical continuity across drug development, enabling teams to generate high‑quality data as molecules, questions, and timelines evolve. Rather than optimizing for a single stage, SCIEX CE platforms emphasize reproducibility, flexibility, and scalability, helping analytical development teams maintain confidence from early research through late‑stage studies.

The multi-capillary BioPhase 8800 system is built for development scientists who need to screen more conditions, generate confident data earlier, and keep pace with expanding pipelines.

The single-capillary PA 800 Plus system is designed for smaller studies, and used throughout the pipeline, including in regulated environments for lot release.

High‑resolution separations with reproducible performance

The PA 800 Plus and BioPhase 8800 systems deliver high‑resolution separations with consistent performance over time. Controlled temperature management, precise injection modes, and standardized capillary formats help minimize analytical variability, supporting reliable comparison of samples across studies and analysts. This reproducibility is critical as development programs move from exploratory analysis to structured assessments of comparability and stability.

Flexible detection to match evolving analytical needs

SCIEX CE platforms support multiple detection modes, including UV and laser‑induced fluorescence (LIF), on both SCIEX CE platforms, and additionally, native fluorescence (NF) on the BioPhase 8800 system. This allows development teams to select sensitivity and detection strategies that align with specific workflows. This flexibility allows for the adaptation of CE methods as analytical requirements change, without abandoning established assays or rebuilding methods from scratch.

Parallel processing for throughput without sacrificing data quality

The BioPhase 8800 system extends throughput capabilities with parallel analysis using multiple capillaries, increasing throughput while maintaining separation quality. This design supports efficient screening and comparison during analytical and process development, helping teams evaluate more samples and conditions within compressed timelines.

Kit‑based workflows that support method consistency

SCIEX CE workflows are supported with validated, kit‑based assays designed to simplify operation and reduce user‑to‑user variability. These standardized workflows help analytical teams establish methods that can be consistently applied and refined as development progresses, maintaining analytical continuity and supporting smoother handoffs between early research, analytical development, and later‑stage studies for multiple modalities.

How this strengthens the lifecycle role of CE

A coordinated CE portfolio gives development teams the flexibility to address distinct workflow demands without compromising consistency or confidence. By combining high‑resolution separations, reproducible performance, flexible detection, and validated kits, SCIEX enables teams to build and extend analytical understanding over time rather than reinventing methods at each stage of the pipeline.

Want to learn more about our solutions?

Explore the BioPhase 8800 system >

Explore the PA 800 Plus system >

Talk to a CE expert >

Bioanalysis across modalities: Advancing confident decisions with modern LC‑MS strategies

As therapeutic pipelines continue to diversify, bioanalysis is being asked to do more than ever before. From small molecules to complex biologics, today’s scientists must generate high‑quality, reliable data across a growing range of molecule types and workflows, often under increasing time pressure.

The rules have changed

Regulated laboratories are evolving faster than ever. New analytical modalities, higher sample throughput, increasing regulatory scrutiny, and leaner teams are reshaping how work gets done. At the same time, expectations for data integrity, standardization, and operational efficiency continue to increase complexity and/or scope. In this environment, LC-MS software is no longer simply an instrument control platform—it has become a critical part of a laboratory’s quality management system. The question is no longer whether your lab has changed, but whether your software has evolved to support the way regulated labs operate today, and if they are ready and able to meet the demands, they will face tomorrow.

The wakeup call

Analyst software has long been a trusted foundation in regulated LC-MS laboratories—and for many, it still performs reliably today. But regulated environments are evolving faster than ever. As labs transition to Windows 11, strengthen cybersecurity policies, modernize IT infrastructure, and prepare for future compliance expectations, software decisions are no longer just about what works today—they’re about managing tomorrow’s risk. Analyst will not be supported on Windows 11. While some labs may continue operating in unsupported environments temporarily, the bigger question is: when that risk becomes reality, will your lab be reacting under pressure—or executing a planned mitigation strategy with confidence?

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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Roxana McCloskey

Where does capillary electrophoresis fit across drug development?

Read time: 4 minutes

Rather than being replaced as programs progress, CE workflows are often adapted and refined, allowing teams to build on familiar data and methods instead of starting over at each stage.

Early development and feasibility: Answering open‑ended questions

In early research and feasibility studies, analytical methods are often exploratory. Molecules, or program direction, may still be changing, and scientists need visibility into unknown or poorly understood attributes.

At this stage, CE is used to:

· Rapidly assess size‑ or charge‑based profiles

· Identify fragmentation, heterogeneity, or integrity issues early

· Screen candidates or conditions with confidence in separation quality

The emphasis is on seeing what’s there, rather than meeting fixed specifications. Quick, high‑resolution separations help avoid false assumptions that can carry over into development.

Analytical and process development: Comparing, optimizing, and understanding change

As programs move into analytical and process development, the role of CE shifts from exploration to comparison. Scientists are focused on asking how and why they are seeing what they are, and if they are different than expectations, why those differences occur.

In this stage, CE is commonly used to:

· Compare lots, conditions, and process changes

· Monitor trends in purity, integrity, or heterogeneity

· Generate data that supports comparability and process optimization

Because CE methods can be tuned for either throughput or resolution, teams can balance speed with data depth as development needs evolve without abandoning the analytical approach they’ve already built.

Late‑stage development and preparation for QC transfer: Building confidence with defensible data

As development progresses toward late‑stage studies, expectations around reproducibility, robustness, and consistency increase. Analytical results must now support external decision‑making, including regulatory discussions and internal handoffs.

At this stage, CE supports:

· High‑confidence characterization for comparability and stability studies

· Robust, reproducible data across time and analysts

· Continuity of analytical understanding from earlier phases

The value of CE lies in data continuity, enabling teams to reference trends and insights established earlier, rather than re‑interpreting results from entirely different methods.

How this strengthens the lifecycle role of CE: One technique, multiple stages, without reinvention

Across all stages, the common theme is not that CE is “early‑stage” or “late‑stage,” but that it provides a stable analytical foundation that adapts as questions become more specific.

By supporting exploratory insight early, structured comparison in development, and defensible confidence later, CE helps biopharma teams reduce analytical friction across the lifecycle even as modalities, timelines, and expectations change.

Why SCIEX CE

CE is used across multiple stages of drug development, not as a single‑purpose analytical technique, but as a platform that adapts as analytical questions change.

Why SCIEX CE is well suited for modern drug development workflows

The multi-capillary BioPhase 8800 system is built for development scientists who need to screen more conditions, generate confident data earlier, and keep pace with expanding pipelines.

The single-capillary PA 800 Plus system is designed for smaller studies, and used throughout the pipeline, including in regulated environments for lot release.

High‑resolution separations with reproducible performance

Flexible detection to match evolving analytical needs

Parallel processing for throughput without sacrificing data quality

Kit‑based workflows that support method consistency

How this strengthens the lifecycle role of CE

Want to learn more about our solutions?

Bioanalysis across modalities: Advancing confident decisions with modern LC‑MS strategies

The rules have changed

The wakeup call

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