This article, the second in a three-part series, highlights industry perspectives on the technological changes and evolving demands impacting chromatography. Read Part 1 here and Part 3 here.
Chromatography automation has evolved from 1960s amino acid analyzers to today’s ultrahigh-performance liquid chromatography (UHPLC) systems. Modern features such as autosamplers and automated flow control enable unsupervised runs and productivity gains across industries.
Now, automation’s role is transforming again, extending beyond robotic sample handling to impact a key stage of the chromatographic workflow. Separation Science connected with top manufacturers to see how automated systems are simplifying challenging sample preparation tasks.
Online Cleanup and AI Solutions
Alan Owens, GC/GC-MS product manager at Shimadzu Scientific Instruments, highlights the growing capabilities of automated sample preparation systems, which can now perform tasks including dilution, filtration, solid-phase extraction (SPE), liquid-liquid extraction (LLE), and derivatization.
Beyond individual tasks, Owens emphasizes the benefits of integrating these automated systems into chromatography workflows through online sample preparation. This approach merges extraction, cleanup, and separation into a single, seamless process, minimizing manual intervention. Many of these systems are also designed to reduce or eliminate solvent use, aligning with green chemistry practices and cutting operational costs.
“Automation in this area greatly reduces human error,” Owens notes. “It is especially beneficial in high-throughput environments, such as pharmaceutical R&D, where consistency and speed are critical.”
Customer demand is fueling innovation in automation throughout the chromatography and mass spectrometry markets, according to John Lesica, president of the chromatography and mass spectrometry division at Thermo Fisher Scientific. For sample preparation, he sees reducing user variability as a key goal for many labs, achieved by automating either select steps or entire workflows.
“Advanced software solutions will also play a critical role in automation,” Lesica adds, “especially when paired with AI tools for analysis.”
Simplifying Workflows with Ready-Made Kits
When asked for an example of how automation is addressing modern separation challenges, Doug McCabe, senior director and portfolio owner at Waters Corporation, points to PFAS (per- and polyfluoroalkyl substances), often called “forever chemicals” due to their persistence in the environment. Historically, weak anion exchange has been the preferred method for isolating PFAS and is embedded in EPA methods such as 533 and 1633. “But it’s a tough assay,” McCabe notes, “because PFAS contamination is so pervasive.”
One solution vendors have developed is the use of stacked cartridges that combine graphitized carbon with weak anion exchange, effectively isolating PFAS while minimizing background interference. These kits come with standards, workflows, and optimized LC-MS protocols to ensure accurate results.
McCabe highlights additional advances in sample preparation, particularly in biopharmaceuticals. The rise of oligonucleotide-based therapeutics has spurred development of extraction kits utilizing weak anion exchange for precise dosing and metabolite tracking. These kits often include SPE plates, traceable reagents, and optimized protocols, allowing for direct LC-MS injection with minimal processing.
Similarly, vendors are streamlining peptide mapping workflows—critical for protein characterization—with kits that cut digestion time from overnight to under 2.5 hours, boosting throughput and consistency.
“Sample preparation is often the most intimidating part of chromatography because it’s manual and introduces variability before analysis even begins,” says McCabe. “Customers want simpler solutions to complex problems, making standardized, streamlined workflows essential.”
Conclusion
Turning one of the most complex areas of chromatography into consistent, efficient workflows is no small feat. Yet, matching customer needs with reliable tools is closing this gap. For more on how automation is reshaping the future of chromatography, continue exploring with Separation Science.
About the Experts
Alan Owens
GC/GC-MS Product Manager, Shimadzu Scientific Instruments
Alan Owens is the GC and GC-MS Product Manager at Shimadzu Scientific Instruments. Alan joined Shimadzu in 2016, with a bachelor’s degree in biology and chemistry, as a GC-MS Product Specialist before ascending to the role of Product Manager in 2021 for GC-MS and 2023 for GC. With over a decade of hands-on experience, Alan Owens has established himself as a distinguished authority in Gas Chromatography and Gas Chromatography-Mass Spectrometry.
John Lesica
President, Chromatography and Mass Spectrometry Division, Thermo Fisher Scientific
John Lesica is the President of Thermo Fisher Scientific’s chromatography and mass spectrometry business. The multi-billion-dollar chromatography and mass spectrometry business, and the 7,000 colleagues under John’s leadership, provide innovative and productivity-enhancing products and services to customers across the globe—supporting those customers with breakthrough innovations from basic research, including proteomics and metabolomics to pharma and biotech to applied markets including clinical, semiconductor, food and beverage, and oil and gas.
Doug McCabe
Senior Director and Portfolio Owner, Waters Corporation
Doug McCabe is the Senior Director and Portfolio Owner, QA/QC at Waters Corporation. Doug leads a
team of product managers, product marketers, applications chemists, and evaluation scientists who
support Waters HPLC and UHPLC customers and systems. Prior to his current role as Portfolio Owner,
Doug led the Chemistry consumables marketing and product management team. Doug has been with
Waters since 2001 when he was hired as product marketing manager of HPLC columns. Throughout his
career at Waters, he has been involved in defining, developing, and commercializing new products that
enable successful chromatographic separations.
