GEN-MKT-18-7897-A
Mar 31, 2026 | Biopharma, BioPhase 8800 system, Blogs | 0 comments
Read time: 3 minutes
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 has earned its place as a foundational assay because it supports high‑value decisions throughout the mAb lifecycle:
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:
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.
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:
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.
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:
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
In biopharmaceutical development, sequence variants (SV) are considered an inherent risk of producing complex proteins in living systems. Sequence variants are unintended changes to the amino acid sequence of a biotherapeutic and can be caused by errors in transcription or translation in the host cell, or cell culture and process conditions. Detailed analysis of SVs is important in process and product development to ensure the drug’s safety and efficacy. Even low‑level sequence variants can have significant implications for product quality, safety, and efficacy, making their accurate detection and characterization a critical requirement across development, process optimization, and regulatory submission.
CE‑SDS remains a cornerstone assay for characterizing fragmentation, aggregation, and product‑related impurities in therapeutic proteins. UV detection has been the long‑standing standard. However, it frequently struggles with baseline noise, limited sensitivity for minor fragments, and subjective integration.
At SCIEX, innovation doesn’t stop at instruments; it extends to how you interact with your LC-MS/MS or CE systems every day. That’s why we’re excited to introduce the SCIEX Now spring 2026 improvements: a set of meaningful enhancements shaped directly by your feedback.
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