Automation Could Help Reduce LC-MS Sample Preparation Bottlenecks
Automation could streamline sample preparation and improve LC-MS workflow consistency.
As mass spectrometry (MS) workflows become faster and more sensitive, one persistent challenge has become increasingly clear: sample preparation is now the primary bottleneck limiting throughput and reproducibility.
With liquid chromatography–mass spectrometry (LC-MS) platforms capable of analyzing samples in under an hour, laboratories are under pressure to modernize upstream processes to match this pace and turn complex preparation steps into reliable, routine workflows.
Few people have a clearer view of this shift than Sarah Simons, the field marketing manager of Automation at Beckman Coulter Life Sciences, a Danaher Operating Company. At ASMS, she spoke about the company’s Biomek™ i-Series—including the newly introduced Biomek i3.
In this conversation, Simons discussed how automation is evolving beyond high-throughput environments, why accessibility is key to adoption, and how labs can address reproducibility, training, and workforce challenges through more approachable systems that help scientists move from sample to answer with greater confidence.
Expanding automation beyond high-throughput labs with the Biomek i3
At ASMS this year, you highlighted the Biomek line, including the new Biomek i3—can you tell me more about what you’re bringing to labs?
Simons positioned the Biomek i-Series not simply as liquid handlers, but as comprehensive solutions for automated assay and sample preparation workflows, designed to help labs make complex, variable steps more consistent and routine. While larger systems such as the Biomek i7 and i5 are designed for high-throughput environments, the i3 expands access to smaller and lower-throughput laboratories.
“It's more than just automated liquid handling; it really is an automated assay preparation system. We're able to provide reproducible and consistent processing for MS sample preparation to a variety of markets,” she said.
A key differentiator is the i3’s compact footprint and simplified implementation. This makes automation viable for labs that may have previously viewed it as too complex, expensive, or unnecessary for their scale, helping more scientists bring routine consistency to workflows that can otherwise slow progress. Despite its smaller size, the i3 retains the same core software and functionality, enabling robust method development and integration with devices such as shakers, heaters, and filtration modules.
“It really does provide that walk-away capability, but in a more compact footprint,” Simons added.
What this means for labs:
- Automation is no longer limited to high-throughput facilities
- Compact systems like the Biomek i3 lower barriers to entry
- More labs can make complex preparation workflows routine, consistent, and reproducible at smaller scales
Addressing the true bottleneck: Pre-analytical sample preparation
How much of the real bottleneck in workflows is happening upstream in sample preparation and handling?
One of the most interesting insights from Simons’ comments is how dramatically workflow constraints have shifted. As analytical technologies accelerate, inefficiencies in sample preparation are becoming more pronounced.
“Upwards of 75% of laboratory time is spent on pre-analytical processing, including sample preparation and the assay prep upstream of the analysis—that's a significant amount of what people are doing,” Simons explained.
Historically, analytical processing itself was the time-limiting step, but advances in LC–MS have reversed this dynamic.
“The bottleneck, from a time perspective, is no longer the analysis. It used to take days to analyze 96 samples, and now it takes less than an hour. This puts the pressure on getting the sample preparation to the same level to keep up with that analysis, so that you can continue your discoveries without having those roadblocks,” she said.
In other words, laboratories that fail to modernize sample prep risk underutilizing their analytical instruments. Automation offers a way to streamline these upstream processes, reducing hands-on time while improving consistency, so that modern analytical platforms can deliver faster, more reliable answers.
“Being able to alleviate the laborious nature of that is pretty impactful for a lot of labs. We're happy to be able to provide a solution upstage that really can help eliminate and help fully utilize the technologies that are being brought into the market from an analysis perspective,” Simons added.
MS workflow bottlenecks:
- Pre-analytical processing accounts for the majority of lab time
- Faster LC–MS systems have shifted bottlenecks upstream
- Manual sample prep limits overall workflow efficiency
- Automation can help labs pair speed with greater certainty in upstream preparation
Overcoming barriers to automation adoption
What’s changed that might shift more labs toward fully adopting automation?
Despite clear benefits, many laboratories have historically hesitated to adopt automation. Simons identified perception as a major barrier—many scientists view automation as overly complex, expensive, or only relevant to specialized environments.
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“I really think that a number of people avoid automation because they see it as something that's complex or large. It's for somebody who's doing high-throughput work, that's not for me,” she said.
Addressing this perception requires both technological and educational shifts. The Biomek i3’s design focuses on accessibility—not just in size and cost, but also in ease of use and training, reflecting a broader move toward automation that enables science rather than complicating it.
“We have several different training options to get people working on the system independently. You don't need to rely on us to automate or to build your methods for you. You're able to do that in your own laboratory,” Simons explained.
Importantly, this also contributes to workforce development, enabling researchers to build valuable automation skills.
Driving greater automation adoption:
- Simplified systems reduce intimidation and complexity
- Training programs enable independent method development
- Automation supports workforce upskilling and career development
- More approachable systems help labs standardize work without slowing scientific progress
Automation as a solution to variability and workforce turnover
Do you see automation becoming standard, or will adoption continue to lag?
Looking ahead, Simons suggested that automation is rapidly becoming essential rather than optional, driven by increasing demands for reproducibility and sensitivity.
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“The need for consistency in your assay preparation is so critical. From the downstream analytical perspective, any variation or inconsistency in the sample preparation itself—you really need those clean samples,” she said.
As analytical systems detect ever smaller differences, even minor inconsistencies in sample preparation can compromise results. Automation minimizes this variability, helping labs standardize workflows across experiments and operators, and making reliable preparation less dependent on individual technique.
Another factor is workforce stability. Laboratory turnover can disrupt projects, particularly when protocols rely heavily on tacit knowledge held by individual scientists.
“When you have a scientist, you bring them in and train them on an assay, that's great. But when that person leaves, then your projects all of a sudden have this huge gap and lag,” Simons explained.
Automation mitigates this risk by embedding workflows into reproducible, software-driven processes that persist beyond individual employees, ensuring continuity in research pipelines and reducing onboarding time for new staff.
“The consistency is really important to continual development and making sure that the pipeline in those discoveries is being maintained,” she said.
Why automation is becoming indispensable:
- High-sensitivity assays require consistent sample preparation
- Automation reduces variability between operators and experiments
- Automation protects against disruption caused by staff turnover
Automation’s role in modernizing laboratory workflows
As laboratory technologies continue to advance, the importance of optimizing upstream processes has never been greater. The introduction of systems like the Biomek i3 highlights a broader shift toward democratizing automation—making it accessible, scalable, and user-friendly for a wider range of laboratories.
Simons’ insights underscore a key message: automation is no longer just about efficiency. It is about enabling reproducibility, supporting workforce development, and helping laboratories turn increasingly complex science into routine, reliable workflows that allow advances in analytical science to deliver answers faster.
Key takeaways
- Automation is moving from a specialized capability to a foundational requirement in modern laboratories.
- Sample preparation now represents the primary bottleneck in LC–MS workflows.
- Accessible systems like the Biomek i3 are expanding automation to lower-throughput labs.
- Reproducibility, consistency, and workforce stability are major drivers of adoption.
- By making complex preparation steps more routine, automation can help labs accelerate reliable answers from advanced analytical workflows.
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