A recent Journal of Pharmaceutical Sciencesstudy by Prof. Susumu Uchiyama and colleaguesat the University of Osaka (Japan), in collaboration with Waters scientists, addresses this challenge by integrating analytical anion-exchange chromatography (AEX) with orthogonal tools including charge detection mass spectrometry (CDMS), mass photometry, LC–MS/MS peptide mapping, and genome integrity assays. Among these, CDMS is pivotal for resolving degradation mechanisms that are otherwise obscured.

Why this study matters

By anchoring chromatographic and spectrometric observations to particle-level measurements, this work demonstrates how CDMS enables confident interpretation of forced degradation data and provides practical guidance for formulation optimization and rAAV quality control.

The core problem: Forced degradation masks multiple pathways

Forced degradation studies are widely used to probe rAAV stability, but similar analytical readouts can originate from fundamentally different molecular failure modes, raising key unanswered questions:

• Which molecular mechanisms underlie changes in AEX retention time and peak area?
• How do pH and temperature redirect rAAV degradation pathways?
• Which degradation processes most strongly impact potency and infectivity?

Why are conventional analytical methods not enough

While analytical AEX is highly sensitive to surface charge changes, interpretation under stress conditions is limited by:

• Similar chromatographic shifts arising from deamidation, aggregation, adsorption, or genome loss
• Mass-averaging techniques that obscure coexisting particle populations
• Increased overlap between empty and full particles as degradation progresses

How does CDMS solve the problem

CDMS overcomes these limitations by directly measuring the mass and charge of individual viral particles. In this study, CDMS revealed that:

• Charge shifts observed by AEX correlate directly with capsid deamidation at the particle level
• Empty and full rAAV particles respond differently to accelerated stress
• Structural rearrangements can counterbalance surface charge changes in genome-containing particles

Distinct degradation pathways across pH conditions

Integration of CDMS with orthogonal techniques revealed sharply distinct degradation regimes:

• Neutral and basic conditions promote deamidation, aggregation, and nonspecific adsorption
• Acidic conditions trigger genome fragmentation, capsid protein cleavage, and rapid titer loss
• A citrate buffer at pH 5.5 provides exceptional thermal stability despite elevated temperature stress

Read the full study, “Forced degradation analysis of recombinant adeno-associated virus serotype 8 based on analytical anion exchange chromatography coupled to orthogonal characterization,” and see how CDMS enhanced rAAV analysis.

A recent Nature Communications study by Prof. Siavash Vahidi and colleagues at the University of Guelph (Canada), in collaboration with Waters scientists, addresses this challenge by integrating charge detection mass spectrometry (CDMS) with native MS, hydrogen-deuterium exchange mass spectrometry (HDX-MS), and nuclear magnetic resonance (NMR). Among these techniques, CDMS is pivotal for resolving the structural heterogeneity that previously obscured the functional mechanism of the bacterial proteasome activator Bpa.

The core problem: Structural heterogeneity masks function

Bpa is a large, ring-shaped regulatory particle that activates the mycobacterial 20S proteasome. Although prior studies identified the dodecamer as the active form, key questions remained unresolved:

• Does Bpa exist exclusively as a dodecamer under physiological conditions?
• How dynamic is Bpa oligomerization in solution?
• Which oligomeric state is responsible for substrate engagement?

These questions arise because Bpa exists as a heterogeneous mixture of dimers, tetramers, and dodecamers that interconvert in a temperature-dependent and reversible manner. Conventional tools such as size-exclusion chromatography (SEC) and native MS struggle to accurately quantify these coexisting species due to charge-state overlap and mass-dependent detection bias.

Why is conventional MS not enough?

While native MS revealed multiple Bpa oligomeric states, interpretation was limited by:

• Overlapping charge-state distributions for high-mass complexes
• Under-representation of large assemblies
• Apparent inflation of low-abundance species

As a result, it remained unclear whether Bpa fully assembles into its functional form under activating conditions.

How does CDMS solve the problem

CDMS overcomes these limitations by directly measuring the mass and charge of individual ions, enabling unbiased analysis of heterogeneous, high-mass protein assemblies. In this study, CDMS demonstrated that under physiological conditions:

• Bpa exists almost exclusively as a fully assembled dodecamer
• Signals from dimers and tetramers disappear

This result resolves inconsistencies seen with conventional MS and confirms that the dodecamer is the dominant, biologically relevant species.

From assembly to function

With the active oligomeric state firmly established by CDMS, the authors could confidently connect structure to function. Supporting techniques revealed that:

• Only dodecameric Bpa engages substrates
• Substrates are recognized via short hydrophobic motifs in disordered regions
• Multiple substrates bind per Bpa ring

Together, these findings show that temperature-dependent assembly acts as a molecular switch that controls when Bpa can deliver substrates to the proteasome.

Read the full study, “Structural heterogeneity and substrate engagement mechanism of the bacterial proteasome activator Bpa,” and learn more about the advantages of CDMS.

A recent Nature Communications study led by Dr. Ronit Mazor and colleagues at the U.S. Food and Drug Administration (FDA), in collaboration with Waters scientists, addresses this challenge by integrating computational immunoengineering with experimental validation. The study introduces a systematic framework for identifying and modifying CD4⁺ T-cell epitopes in the AAV9 capsid while preserving vector function.

Why this study matters

This work provides a compelling proof-of-concept for rational deimmunization of viral vectors. By integrating computational prediction with detailed experimental validation, the study establishes a scalable framework for improving the safety, durability, and re-dosing potential of AAV-based gene therapies.

The core problem: Capsid-driven T-cell responses limit gene therapy

Key questions driving this study included:

• Which regions of the AAV9 capsid act as immunodominant CD4⁺ T-cell epitopes?
• Can these epitopes be disrupted without compromising capsid integrity or transduction efficiency?
• How can candidate mutations be identified systematically rather than by trial-and-error?

Why are conventional strategies not enough

Previous approaches to reducing AAV immunogenicity are limited by:

• Incomplete control over T-cell–mediated immune recognition
• Dependence on naturally occurring non-immunogenic serotypes
• Lack of scalable, systematic methods for epitope redesign

How does computational epitope engineering solve the problem

Using the Epitope Modification and MHC Prediction (EMMP) pipeline, the study demonstrated that:

• A CD4⁺ T-cell epitope centered on residue R312 is immunodominant in the AAV9 capsid
• EMMP can systematically evaluate mutations predicted to reduce MHC class II presentation
• R312H and R312Q emerged as leading candidates for experimental validation

From prediction to biological validation

Experimental testing revealed that:

• The R312Q mutation abolishes CD4⁺ T-cell activation and cytokine production
• Anti-AAV9 antibody responses are significantly reduced
• Vector biodistribution is preserved with only modest reductions in transduction efficiency

Read the full study, “Integrated computational and experimental immunoengineering of adeno-associated virus capsid T-cell epitopes in mice,” and learn more about the latest developments in AAV analysis.

The key is knowing what really matters as you evaluate your options.

Trusting the foundations: Data security, integrity, and compliance

Data sits at the heart of every lab, and understandably, it’s often the first concern when considering cloud adoption. For some, handing over responsibility for data storage can feel like a loss of control.

In reality, the right SaaS provider should enhance your control, not reduce it. Strong providers, like Waters, build platforms around security and compliance from the ground up, embedding best practices into everyday use rather than treating them as add-ons.

When assessing vendors, it’s worth focusing on a few critical areas:

• How data is encrypted both in transit and at rest
• The level of auditability and traceability built into the system
• Compliance with standards such as SOC 2® Type II, ISO 27001, and other, third-party risk assessments
• How user access and permissions are managed

A well-designed cloud platform often brings a level of consistency and robustness that’s difficult to maintain internally.

Scaling without friction

Growth is a positive challenge—but it can quickly expose the limitations of traditional systems. Whether it’s increasing sample volumes, new instrumentation, or expanding across sites, many on-premises platforms struggle to keep pace without significant intervention.

Cloud software changes that dynamic. It allows labs to expand naturally, without the need for new servers, complex upgrades, or long lead times. New users can be added quickly, additional workflows configured with minimal disruption, and multi-site operations supported more seamlessly. What this really means is that your systems stop being a constraint. Instead, they become an enabler of growth.

Looking beyond the headline cost

Cost is often one of the first comparisons made—and one of the most misunderstood. While SaaS introduces a subscription model, the true comparison lies in the total cost of ownership over time. On-premises systems come with ongoing demands that are easy to underestimate: maintaining hardware, managing backups, handling upgrades, and allocating internal IT resources.

Cloud solutions shift much of that burden externally. It’s not just about reducing costs, but about making them more predictable and easier to manage. A useful way to frame the decision is to consider:

• The hidden operational costs that are tied to your current system
• The internal effort required to maintain and support it
• The financial and operational impact of downtime or system failures

Often, the value of SaaS becomes clearer when these factors are taken into account.

Creating a connected lab environment

Laboratories rarely operate with a single, isolated system. Instruments, laboratory information management systems (LIMS), electronic notebooks (ELNs), reporting tools, and business systems all need to exchange data efficiently. Cloud platforms are typically designed with this interconnected reality in mind. They make it easier to integrate systems, automate data flows, and reduce manual intervention.

That said, it’s important to look closely at how any new solution will fit into your existing ecosystem. Considering things like whether the platform offers modern APIs for integration, how easily it can exchange data with your current systems, and the flexibility to adapt as your technology landscape evolves is important.

The goal isn’t just to replace one system, it’s to create a more cohesive and efficient digital environment.

With on-premises solutions, data remains in a silo, and it can be difficult to consolidate instruments, software, and collaborators. Software solutions built on cloud platforms can overcome these challenges. With Waters Data Intelligence Software, you can reduce risk and strengthen data integrity, while maintaining confident audit-readiness through dynamic dashboards that enable vigilant monitoring of key data integrity measures, which reduces the high cost of audit preparation and the risk of adverse findings. Cloud solutions like Waters System Monitoring Software support scalability of your lab by providing detailed information on the usage and performance of instruments, so you can optimize system and lab efficiency and make data-driven decisions on your lab productivity. Finally,  cloud technologies, like Empower Data Viewer take the connected lab even further by providing the capability to share data across labs and partners and easily grant your team members or partners worldwide, web-based access to explore data, minimizing productivity delays.

Adoption hinges on user experience

User experience plays a critical role in whether a new platform is embraced or resisted. Cloud-based software has, in many cases, raised the bar here. Cleaner interfaces, browser-based access, and more intuitive workflows can make a noticeable difference to day-to-day usability. This isn’t just about convenience. Better usability leads to:

• Faster onboarding for new team members
• More consistent data entry
• Reduced errors and workarounds
• Higher overall engagement with the system

Ultimately, the success of any software investment depends on the people using it.

Choosing a partner, not just a platform

One of the defining characteristics of SaaS is that it evolves continuously. Updates are delivered regularly, features improve over time, and the platform grows alongside its users. That makes your choice of provider particularly important. You’re not just selecting a system as it exists today; you’re aligning with a team that will shape its future.

The right partner won’t just deliver software—they’ll help you keep moving forward.

Moving forward with confidence

Adopting cloud software doesn’t have to be a leap into the unknown. Many laboratories take a phased approach, building confidence over time and expanding their use as they see value. What matters most is having the right guidance at each stage—from initial evaluation through to implementation and beyond.

At Waters, we work with laboratories to make that journey practical, manageable, and worthwhile. Our focus is not just on delivering cloud solutions, but on supporting the people and processes that make them successful.

Because moving to the cloud isn’t just about modernizing your technology. It’s about creating a lab that’s ready for whatever comes next. Learn more about Waters Cloud Platform and our software solutions.

Or, if you’d like to take the next step, arrange a demo of any of our cloud software solutions:

Arrange a Demo of Waters System Monitoring Software

Arrange a Demo of Waters Data Intelligence Software

Arrange a Demo of Empower Data Viewer

At the center of this process are critical quality attributes (CQAs), the measurable properties that define whether a drug meets its required standards.

In this blog, we break down the role of CQAs in biologics development and how advanced particle analysis is enabling deeper insight, earlier decisions, and continuity from development through QC.

What are critical quality attributes?

A CQA is any physical, chemical, biological, or microbiological property that must remain within a defined range to ensure product quality.

CQAs typically fall into three categories: 

• Physical characteristics: these include aspects such as the size and shape of the pharmaceutical product 
• Chemical properties: these encompass elements like the pH level and concentration of the drug 
• Biological attributes: these involve factors such as sterility and bioburden levels in the product 

The process of identifying CQAs is an essential step in the drug development process as it ensures that the final drug product is consistent, effective, and safe for patient use.² Any deviation can influence the efficacy of a drug, potentially leading to harmful effects on the patient. 

Moreover, the recognition of CQAs is not just a best practice; it’s a regulatory mandate. Regulatory authorities, including the FDA and the European Medicines Agency (EMA), require the identification of CQAsas part of the drug development process.³ This ensures that drug products meet the necessary quality standards and are safe for consumption.⁴ 

CQAs and Quality by Design

CQAs are foundational to Quality by Design (QbD), a framework that emphasizes building quality into a product from the start, rather than testing for it at the end.

QbD relies on deep process understanding, identification of risk factors, and control strategies tied directly to CQAs. In practice, this means CQAs must be measured accurately, consistently, and across every stage of development, not just at release.

The Challenge: Subvisible Particles as a Critical CQA

One of the most challenging CQAs in biologics is subvisible particles.

These particles often fall in the ≥10-µm range and can:

• Reduce stability and shorten shelf life
• Trigger immune responses or adverse events

Because of this, they are closely monitored throughout development and in QC environments. Subvisible particle analysis is also central to meeting compendial requirements, such as USP <788> and USP <789>, which define limits for particulate matter in injectable drug products and set expectations for particle counting and size classification.

Despite their importance, traditional methods have struggled to provide actionable insight, especially in early-stage, low-volume conditions. This creates a gap across the workflow, with limited insight into development, different methods required in QC, and disconnected datasets across the product lifecycle.

Closing the Gap with Advanced Particle Analysis

The Aura Particle Analysis System addresses this gap by enabling high-resolution particle characterization from development to QC across various therapies – including biologics, AAVs, LNPs, and cell therapies.

Using Backgrounded Membrane Imaging (BMI) and Fluorescence Membrane Microscopy (FMM), Aura delivers precise particle count, size distribution, morphology, and particle identification.

Importantly, Aura supports both:

• Small-volume analysis with as little as 5 µL for early-stage work
• Large-volume workflows supporting over 500 µL per sample to align with QC expectations

This allows teams to generate meaningful CQA data earlier, maintain one method across stages, and build a continuous dataset from formulation through release.

A More Complete View of CQAs

By providing deeper visibility into subvisible particles, one of the most complex CQAs, the Aura System enables earlier detection of instability or aggregation, better differentiation between particle types, and more informed decision-making throughout development.

Instead of reacting to CQA failures late, teams can design around them from the start.

Conclusion

CQAs are the foundation of drug quality, but their value depends on how well they are understood and controlled.

As biologics grow more complex, the need for technologies that can deliver accurate, consistent, and stage-spanning insight continues to increase.

With advanced particle analysis, it is now possible to move from fragmented workflows to a single, continuous understanding of CQAs across the development process.

References

1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4070262/#CR3 

2. https://www.linkedin.com/pulse/benefits-identifying-critical-quality-attributes-cqas-mo-heidaran-2e/ 

3. S. Department of Health and Human Services, Food and Drug Administration, Center for Drug Evaluation and Research (CDER). Guidance for Industry: Q8(R2) Pharmaceutical Development. November 2009. 

4. https://www.roosterbio.com/blog/critical-quality-attributes-cqas-know-their-importance-limitations-in-product-process-development/ 

This raises important questions about insulin aggregation: does insulin, once diluted and left in a saline bag, start to clump? And if it does, would anyone be able to detect it?

A study led by Professor Luís Maurício Trambaioli R. Lima at Universidade Federal do Rio de Janeiro addressed this using dynamic light scattering (DLS), a technique known for its exceptional sensitivity to early-stage aggregation. Using a DynaPro DLS Instrument, the team evaluated insulin stability under conditions mimicking real clinical workflows.

DLS measures fluctuations in scattered light caused by particles undergoing Brownian motion. The physics of light scattering means larger species scatter disproportionately more light, enabling highly sensitive aggregate detection. To establish detection limits, the researchers created a reference sample of aggregated insulin as a benchmark, then diluted it stepwise to determine how far the signal could still be detected.

The results were striking. Using a DynaPro DLS Instrument, aggregated insulin remained detectable down to 0.05 units/mL—nearly a 10,000-fold dilution, and just 5% of the standard clinical infusion concentration. This demonstrates that DLS can identify insulin aggregation at levels 20-fold below what is typically administered to patients.

With this sensitivity established, the team evaluated insulin diluted to 1 unit/mL in saline over extended periods. While clinical guidelines recommend replacing infusions every 24 hours, the study monitored samples for up to 72 hours. No aggregates were detected throughout this timeframe, indicating strong conformational stability under IIP conditions.

These findings are significant not just because insulin remained stable, but because the measurement technique is sensitive enough to detect problems far below clinically relevant levels.

By combining high sensitivity with a plate-based format, the DynaPro Plate Reader enables efficient, low-volume, and high-throughput monitoring of protein therapeutics.

For a deeper look at the experimental design, detection limits, and detailed insulin aggregation analysis, refer to the full study:

Physicochemical Stability of Insulin and Analogues in Saline Infusion: Screening for Amyloid and Amorphous High-Molecular-Weight Material, ACS Omega 2026, 11, 10, 16481–16488, https://doi.org/10.1021/acsomega.5c12466

Request additional information and learn more about the DynaPro Plate Reader.

But why solid‑core particles are more efficient is often misunderstood.

Let’s separate reality from misconception with two truths and a lie about solid‑core particle efficiency.

Truth #1: Longitudinal diffusion plays a major role – but not for the reason you might think

Yes, solid‑core particles exhibit reduced longitudinal diffusion. But the reason has little to do with a shorter diffusion path length.

The real driver is the mobile phase volume inside the particle.

In a fully porous particle, analytes can diffuse throughout the entire internal pore volume. That gives the sample band more space to spread out along the column length.

In contrast, a solid‑core particle contains an impermeable core, which dramatically reduces the volume inside the particle that is accessible to the mobile phase. With less internal space for analytes to explore, longitudinal diffusion is naturally limited.

The result:

• Less band broadening
• Sharper peaks
• Higher efficiency—especially for small molecules operating at or below the optimum flow rate

Truth #2: Eddy dispersion, particle morphology, and packing uniformity significantly impact efficiency

One of the most underestimated contributors to efficiency is how particles pack inside the column.

In any packed bed, the structure near the column wall differs from that in the center. These structural differences create variations in flow velocity across the column radius, which contribute to eddy dispersion.

This is where solid‑core particles used within solid core HPLC columns have an advantage.

Because of their surface characteristics, particularly increased surface roughness, solid‑core particles pack more uniformly across the column diameter than smoother, fully porous particles. A more homogeneous packed bed leads to:

• A more consistent flow velocity profile
• Reduced radial heterogeneity
• Less band broadening caused by eddy dispersion

This improved packing uniformity can make a meaningful contribution to efficiency gains.

The Lie: Solid‑core particles are more efficient because they significantly reduce mass transfer resistance

This is more of a misconception than an outright lie. Mass transfer plays a smaller role in solid-core efficiency than it is usually credited with.

The argument goes like this: solid‑core particles have a thin, porous layer around a solid core, which shortens the diffusion path inside the particle, which in turn reduces the mass transfer resistance for the analyte (the C-term in the Van Deemter equation).

Shorter path equals less mass transfer resistance, which equals higher efficiency.

That sounds reasonable, but it doesn’t hold up when you look at the data closely.

• For small molecules: Mass‑transfer resistance is already very low for both fully porous and solid‑core particles. At typical flow rates, differences in solid‑to‑liquid mass transfer are negligible — certainly not large enough to explain the consistently higher efficiency observed with solid‑core materials.

• For large molecules: It is true that shorter diffusion paths in the porous shell can improve mass transfer. However, even in this case, mass transfer is not the only contributor to the overall efficiency gain.

So, while reduced mass transfer resistance exists, it plays a relatively small role in the improved efficiency of a solid‑core particle.

The bottom line

When you put everything together, the efficiency advantage of solid‑core particles comes down to two main contributors:

1. Eddy dispersion – More uniform packing leads to a more consistent flow profile distribution and reduced band broadening.
2. Longitudinal diffusion – Reduced mobile phase volume inside the particle limits band broadening and sharpens peaks.

Mass transfer can contribute to efficiency, but it is not the primary driver of solid-core particle performance. Shorter diffusion paths in the porous shell can reduce mass transfer resistance for large molecules, but for small molecules this impact is minimal.

So, the next time someone says solid‑core particles are more efficient because of improved mass transfer, you’ll know the truth!

For more on the benefits of solid-core particles, check out the following resources:

Infographic: Upgrading to Solid-Core Particles

Video: What Drives Higher Efficiency in Solid-Core Columns?

Application Note: Improving Separation Efficiency with CORTECS Premier Columns that Feature Solid-Core Particles

Blog Post: The Quest for Maximum LC Performance

Waters next generation GTxResolve MaxPeak Premier Microflow Columns represent one such leap forward. Engineered to enhance recovery for challenging biomolecules, including oligonucleotides, they offer a high-sensitivity path to deeper insights even when the sample size is limited.

Why microflow for oligonucleotide analysis?

Oligonucleotide characterization presents unique chromatographic challenges, including:

• Adsorptive losses to metal hardware
• Poor peak shapes for acidic or highly charged analytes
• Sensitivity constraints when working with scarce therapeutic samples

Shrinking column diameter from 2.1 mm to a 1 mm ID microflow format directly addresses these issues by reducing band broadening and concentrating analytes for improved detectability. Waters newest microflow columns deliver up to 2x higher sensitivity than conventional stainless-steel microflow columns, an advantage especially meaningful for low-abundance oligonucleotides, often associated with bioanalysis/DMPK studies.

MaxPeak HPS Technology: Protecting every molecule

As has been clearly shown with traditional 2.1 mm ID analytical columns, MaxPeak High Performance Surfaces (HPS) Technology essentially eliminates the variability associated with non-specific adsorption (NSA) of acidic analytes (including oligonucleotides) to the metal surfaces of a column, thus improving recovery/sensitivity and repeatability.

For oligonucleotides that are often highly negatively charged, this translates into:

• Reduced analyte loss due to minimized metal interactions
• Sharper, taller peaks
• Improved reproducibility and lower limits of detection

These improvements allow analysts to move confidently from method development to validated performance without the lengthy passivation/sample conditioning associated with conventional stainless-steel hardware.

Efficiency with purpose: Lower sample and solvent use

In addition to sensitivity enhancements, microflow formats help laboratories meet sustainability and cost-reduction goals. Transitioning from a 2.1 mm to a 1 mm ID column reduces:

• Solvent use by 4X, lowering waste and operating expenses
• Sample consumption by up to 75%, allowing more data to be captured from precious, limited samples

With reproducibility from the first injection and reduced peak tailing at low flow rates, these columns integrate seamlessly into LC-MS oligo workflows without requiring major system reconfiguration. 

A more sustainable future for oligonucleotide characterization

Beyond performance, MaxPeak Premier Microflow Columns are manufactured with sustainability in mind. They incorporate up to 70% recycled content and come from resource-efficient facilities certified for environmentally responsible design. In addition to the solvent reductions inherent to microflow separations, MaxPeak Premier Microflow Columns received the ACT Label certification for their environmentally responsible design and manufacturing.

Microflow is no longer a compromise, it’s a competitive advantage

As oligonucleotide therapeutics continue their rapid expansion, analytical teams need tools that can keep pace with increasing complexity and decreasing sample volumes. MaxPeak Premier Microflow Columns bring together heightened sensitivity, improved analyte recovery, and meaningful resource savings, delivering the workflow acceleration and data confidence required in modern bioseparations.

Whether you are developing ASOs, siRNAs, CRISPR guides, or mRNA purification strategies, microflow are your high-performance, low-resource path forward.

Are you ready to explore what’s possible with GTxResolve Microflow Columns? Take a deeper dive with these resources:

• Register for our upcoming microflow webinar
• Visit our Microflow Columns product page
• Download our infographic

That’s where advances in Protein A (ProA) affinity chromatography are making a meaningful difference, reshaping how teams measure titer, monitor cultures, and assess product quality throughout development.

How affinity chromatography and Protein A work

Affinity chromatography leverages highly specific biological interactions to isolate a target molecule from a complex mixture. In the case of monoclonal antibodies, Protein A, a bacterial protein, binds strongly to the Fc region of many IgG subclasses.

The workflow is simple and powerful:

1. Antibodies bind to immobilized Protein A
2. Impurities wash through
3. Bound antibodies elute in a concentrated, measurable form

This selectivity has made Protein A the backbone of antibody analytics for decades, widely used for titer measurement, purification, variant analysis, and bioprocess monitoring.

Where modern Protein A affinity chromatography delivers real impact

1. Earlier, more sensitive titer measurement

One of the biggest challenges in upstream development is waiting for cultures to reach concentrations detectable by traditional assays. Newer Protein A workflows allow teams to measure titer from microbioreactors much earlier in cell culture (even as early as day 1), giving them faster visibility into growth trends, clone performance, and culture stability.

This earlier insight helps teams:

• Make informed selections sooner
• Identify issues before they affect yield
• Reduce delays and unnecessary repeat experiments

2. Lower carryover for more trustworthy titer results

Carryover, remnants of mAbs or impurities left behind after elution, can undermine result reliability and contaminate follow-up injections. Updated Protein A column designs now significantly reduce this issue.

Key advantages:

• ~65% lower carryover vs. a comparable alternative, meaning cleaner injection-to-injection performance
• More accurate, reproducible titer data for sequential samples
• Lower risk of cross-contamination during column reuse, protecting downstream analyses

3. Integrated titer and aggregate analysis through 2D ProA–SEC

Traditional workflows require separate assays for titer and aggregate/size-variant analysis. Modern two-dimensional Protein A–SEC methods bring these measurements together, providing both readouts in a single run.

These integrated workflows offer:

• Titer and aggregate data from one injection
• High throughput without adding complexity
• Optimization of speed or resolution depending on your needs

Options range from trap-and-elute formats for speed and high resolution to direct-connect approaches designed for simplicity. Both reduce hands-on work and streamline data collection.

4. Faster, deeper structural insight with ProA-MS

Teams increasingly need structural understanding beyond just titer. Rapid Protein A elution combined with native high-resolution MS now enables intact mass analysis of mAb and msAb variants directly from cell culture media in less than five minutes.

This approach reveals:

• Low-abundance variants
• Oxidation states
• Heavy chain pairing differences
• Other structural attributes normally require additional purification

The ability to pair titer and structural insight so quickly helps scientists make smarter decisions earlier in development.

5. Stronger support for upstream and downstream monitoring

Bioprocessing teams need analytics that are fast, stable, and compatible with a wide range of LC conditions. Updated Protein A methods maintain reproducible performance under high-pressure operation and across long study timelines, making them well-suited for:

• Real‑time titer trending on both HPLC and UPLC systems
• Early feedback for process optimization
• Routine monitoring across multiple batches

The consistency they provide is essential for robust process development and PAT initiatives.

6. More consistent performance through routine CIP

Media components inevitably accumulate Protein A resin over repeated injections, affecting backpressure, peak shape, and recovery. Routine clean-in-place (CIP) keeps columns stable and prevents buildup. In controlled testing, Protein A columns remained effective for 1500+ injections when CIP was applied regularly.

Benefits include:

• Sustained performance over long campaigns
• Reduced fouling and drift
• Longer column lifetime
• More consistent titer data

The takeaway: Protein A is evolving alongside modern bioprocessing.

Modern Protein A affinity chromatography has become a multi‑functional analytical engine that helps teams achieve:

• Earlier visibility into process performance
• Cleaner, lower-carryover workflows
• Integrated multi-attribute analysis
• Faster structural insight
• Longer lasting, more stable columns

As biologics pipelines accelerate and diversify, these capabilities are no longer ‘nice to have;’ they’re essential for keeping development on track, minimizing risk, and improving overall process understanding.

Learn more about Waters BioResolve Protein A Affinity Columns featuring MaxPeak Premier Technology.

Global supply chains, the rise of outsourced partnerships, hybrid working models, and the relentless pressure to do more with less are reshaping how laboratories operate. Against this backdrop, many organizations are realizing that the traditional perpetual software model no longer gives them the agility or efficiency they need.

That’s where Empower Subscription options come in. By combining the proven Empower CDS with modern, cloud-enabled capabilities such as the waters_connect System Monitoring Application, Empower Data Viewer, and, in the ES5 top subscription tier,  machine learning-powered Anomaly Detection— the subscription model is built to support the evolving demands of modern science.

So what does this shift mean in practice? Let’s explore what Empower Subscription is, why laboratories are embracing it, and how it can transform the way you work.

A Practical Way to License Empower Software

With Empower Subscription, instead of purchasing perpetual licenses, laboratories subscribe to tiered bundles that include core Empower CDS Software plus cloud-enabled tools and services. This approach delivers easy access to current software while simplifying how labs plan, budget, and scale their informatics.

Predictability and Control of Costs

Budgets are always tight in the lab. Capital-intensive perpetual licenses can put pressure on finances, with heavy upfront costs followed by unpredictable spending on maintenance or upgrade projects. Subscriptions replace this with a smoother, more predictable model.

Instead of dealing with large financial outlays for each individual software product, subscriptions allow labs to pay a steady, manageable subscription fee, often bundling several software products together for ease and value for money. This makes it easier for finance leaders to forecast spending and for lab managers to plan resources. Just as importantly, it aligns cost with value: you’re paying for ongoing access to a service that is always current and continuously improving. Subscriptions can also improve service efficiency. For example, offerings like the Waters Professional Services Subscription Plans reduce the cost of deploying an upgrade and offer reassurance that support is available when you need it.  

Keeping Your Fleet Running Smoothly

Every lab leader knows the frustration of discovering that an instrument has been idle, in error, or under-utilized for hours…or even days. These inefficiencies add up quickly, delaying results and creating bottlenecks.

With the waters_connect System Monitoring Application— included in every Empower Subscription bundle— supervisors gain real-time visibility into instrument status across their fleet. They can see instantly whether a system is running, idle, or in need of attention. Alerts notify staff the moment something goes wrong, allowing issues to be resolved before they cause costly downtime. The result is better throughput, faster troubleshooting, and smarter use of existing assets. Instead of reacting to problems after the fact, labs can take a proactive approach to instrument management.

Collaboration Without Barriers

Science is no longer confined to one lab or one team. Pharmaceutical companies work with CROs and CDMOs, research organizations collaborate across continents, and hybrid working means analysts and reviewers aren’t always on-site. Yet too often, data sharing still relies on outdated practices, exporting chromatograms, emailing PDFs, or juggling multiple Empower Software versions across sites. These methods are slow, cumbersome, and introduce risks.

Empower Data Viewer, available in ES3 and ES5 bundles, changes this dynamic. It allows chromatographic data to be accessed securely through a browser, without the need for local Empower Software installations. Results can be viewed in near real time, and because it supports multiple Empower Software versions, labs can harmonize data across sites even during phased migrations. This improves transparency, accelerates communication with partners, and makes collaboration seamless. Instead of waiting for emailed reports, stakeholders can see results as they happen, wherever they are.

Faster Data Review with Machine Learning

Manual chromatogram review is one of the most time-consuming parts of a laboratory workflow. Analysts spend hours scanning files, even though most chromatograms are routine. With sample volumes only increasing, review often becomes a bottleneck.

The machine learning-powered Anomaly Detection feature in the ES5 bundle addresses this challenge directly. By automatically flagging chromatograms that deviate from expected patterns, it allows analysts to focus their attention where it’s needed most. The system highlights what triggered the anomaly, whether it’s a shift in retention time, an unusual peak, or another irregularity, so the root cause can be investigated quickly.

Future-Proofing Your Laboratory

Perhaps the most compelling reason to move to subscription is the future. Science is accelerating, and laboratories need tools that can evolve with them. Our subscription bundles ensure you’re always positioned to benefit from the next wave of innovation whether that’s machine learning capabilities, broader monitoring across instruments, performance and results, or new ways to visualize and interpret data. By choosing Empower Subscription, you’re not just upgrading your CDS, you’re investing in a model that keeps your laboratory competitive, agile, and ready for whatever comes next.

A Better Way to Run Your Lab

Perpetual software licenses have played a vital role in laboratories worldwide, but they reflect an earlier era of science that was more predictable in terms of funding, resourcing, and pace of scientific advancement. Today, businesses are required to respond to rapidly changing external factors that will affect their capital, resourcing, and resulting scientific outcomes. High upfront investments are now viewed as a risk, so subscriptions are introduced as a flexible way to respond to those changing factors. For laboratories ready to move faster, work smarter, and prepare for the future of informatics, subscription isn’t just a new way to license software, it’s a better way to run your lab.

Discover How Empower Subscriptions can Transform Your Lab Operations

Read our new whitepaper to explore the benefits, features, and real-world impact of Empower Subscriptions.

Ready to talk to someone about making to move to Empower Subscriptions? Click here to arrange to speak to a Waters representative.