Roxana McCloskey

CE‑SDS in monoclonal antibody therapeutic development

Mar 31, 2026 | Biopharma, BioPhase 8800 system, Blogs | 0 comments

Read time: 3 minutes

A familiar assay with a new way to see more.

In monoclonal antibody (mAb) development, assessment of purity and integrity of the protein in question is critical. CE‑SDS is the gold standard assay and is routinely run from analytical development through QC and lot release. It’s trusted because it consistently delivers quantitative, size‑based insight into purity and fragmentation, and it fits naturally into regulated environments.

What continues to evolve with the changing drug landscape isn’t whether teams use CE‑SDS, but how much more they need from it: more confidence in low‑level species, less time spent wrestling with baselines and integration, and greater consistency across analysts, instruments, and sites.

This is where modern execution, and especially modern detection, start to matter.

CE‑SDS: A workflow that underpins decisions

CE‑SDS has earned its place as a foundational assay because it supports high‑value decisions throughout the mAb lifecycle:

Analytical development: establishing robust purity/fragmentation methods and acceptance criteria
Process development: tracking how upstream/downstream changes influence fragments and clipped species
Stability and comparability: trending subtle shifts over time or across process changes
QC and lot release: confirming batches meet specifications with regulator‑familiar reporting

Why keep raising the bar for a routine assay?

Even for established programs, size and purity assessment still create persistent analytical pressure. Fragmentation, clipping, mispairing, and partial assembly are not rare events; they’re known risks that must be monitored and controlled.

CE‑SDS remains uniquely valuable because it provides complementary views under two common conditions:

Reducing CE‑SDS: resolves heavy and light chains to quantify chain integrity and fragmentation
Non‑reducing CE‑SDS: assesses intact antibody and clipped species

As mAb formats expand and timelines tighten, teams increasingly rely on CE‑SDS not just to determine “what’s there,” but for trend confidence. Analytical teams need the ability to compare across runs, days, and sites without second‑guessing the data.

The real bottleneck: data confidence at low levels

In many labs, CE‑SDS isn’t limited by separation efficiency. It’s limited by how confidently low‑abundance species can be detected and reliably quantified.

When detection baselines drift or noise complicates integration, analysts spend time:

Re‑integrating peaks and debating thresholds
Re‑running samples to confirm borderline species
Explaining variability during comparability or method transfer
That friction doesn’t just slow the lab—it slows decisions.

What is new: Native fluorescence detection (NFD) for CE‑SDS

While CE‑SDS is a well‑established workflow, native fluorescence detection (NFD) for CE‑SDS is a newer capability unique to the .

NFD leverages the intrinsic fluorescence of proteins to deliver label‑free detection with a cleaner baseline and improved sensitivity compared with traditional UV approaches, helping teams see low‑level species with greater confidence.

NFD can improve routine analysis by reducing ambiguity in peak detection and integration. It can match the sensitivity gained from LIF detection with dye, but without adding the sample preparation time and variability associated with labeling.

At SCIEX, NFD is available as a detection option on the BioPhase 8800 system , enabling teams to pair a trusted CE‑SDS workflow with a more sensitive, lower‑noise view of their data.

A more modern mindset. Don’t replace CE‑SDS, strengthen it

In a world where drug development programs move fast and data must travel across and throughout organizations, the analytical teams that win are the ones that generate results people can trust.

Teams don’t need to rethink whether CE‑SDS belongs in their control strategy. They need to ensure it continues to deliver what modern development demands:

Consistent, reproducible results across analysts and sites
Confidence in low‑level impurities and fragments
Faster decisions with less time spent on manual data cleanup

That’s why the most impactful innovations in CE‑SDS today aren’t about replacing the workflow; they’re about improving how reliably and efficiently it performs.

CE‑SDS will remain the gold-standard assay for protein purity and integrity. The opportunity is to make it a higher‑confidence daily assay—by modernizing execution and adopting detection that helps visualize the information more clearly, earlier.

Watch our webinar: https://sciex.com/Hidden/landing-pages/nfd-launch-content-hub

Read the technical note: https://sciex.com/tech-notes/biopharma/intermediate-precision-study-of-ce-sds-assay-on-biophase8800-with-native-fluorescence-detection

3 reasons ZT Scan DIA is changing the game in metabolomics

For years, metabolomics researchers have faced a frustrating reality: modern high-resolution mass spectrometers can detect tens of thousands of molecular features, yet only a fraction can be confidently identified. The challenge is no longer finding molecules. It is generating the high-quality MS/MS data needed to confidently assign structures and extract meaningful biological insights.

ADC analytics FAQs: Answering the most common questions about ADC characterization

Antibody-drug conjugates (ADCs) have emerged as one of the fastest-growing classes of biotherapeutics, combining the targeting specificity of monoclonal antibodies with the potency of cytotoxic payloads. However, this unique architecture also introduces significant analytical complexity. From drug-to-antibody ratio (DAR) distributions and charge variants to conjugation sites and structural modifications, ADCs present multiple, interconnected sources of heterogeneity that must be understood to ensure product quality and performance.

Sterile but toxic: Cereulide detection in food matrices

In a recent webinar, Ming Gao, Ph.D., Senior Research Chemist at Mérieux NutriSciences, explored the growing challenge of cereulide contamination in food products and the analytical strategies needed to detect this heat-stable toxin at trace levels. The session examined how LC-MS/MS can help laboratories overcome the limitations of traditional microbiological screening and meet emerging regulatory requirements.

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.

0 Comments