How automated mass spectrometry is expanding clinical lab capacity

Mass spectrometry (MS) offers clinical laboratories the ability to identify and quantify a wide range of biomolecules with exceptional specificity and sensitivity. When coupled with liquid chromatography, mass spectrometry can readily distinguish compounds that may challenge conventional immunoassays, such as steroid hormones or compounds present at low concentrations.¹

Mass spectrometry’s analytical advantages have made it valuable in the fields of endocrinology, toxicology, therapeutic drug monitoring, and more. Yet analytical power alone is not sufficient to drive widespread adoption. Complex sample preparation, challenging workflows, and time-intensive data review have limited implementation of mass spectrometry in clinical labs around the world. Fortunately, these constraints are being addressed by new emerging technologies that have streamlined and automated mass spectrometry workflows, improving the accessibility and scalability of this valuable analytical technique.

Lowering the implementation barrier

Liquid chromatography and mass spectrometry are often used together to detect and quantify important molecules in biological samples. Liquid chromatography sorts molecules by physicochemical properties, while mass spectrometry ionizes molecules to determine their mass-to-charge ratio. The analytical power of mass spectrometry can be enhanced by combining two analyzers into one instrument, which is known as tandem mass spectrometry. One of the most commonly employed mass spectrometry approaches,² this combination of techniques is referred to as LC-MS/MS.

Adoption of LC-MS/MS by clinical laboratories has historically required significant investment. The reagents for mass spectrometry workflows are often sourced from multiple suppliers, which requires clinical labs to develop their own laboratory-developed tests (LDTs). To build LDTs, labs must design and rigorously test multiple components of LC-MS/MS assays, including sample preparation, optimization of chromatography columns and mobile phases, and the establishment of reliable calibration techniques. Furthermore, mass spectrometry protocols can vary significantly between analyte categories, requiring labs to develop new tests if they want to expand their analytical offerings.

Fortunately, biotechnology companies have developed kits and columns that can alleviate the need to design assays in-house. For example, new paramagnetic microparticles can simplify sample prep by selectively capturing analytes from complex biological matrices. Pre-optimized high-performance liquid chromatography (HPLC) cartridges are now commercially available, eliminating the need for in-house development of these columns. The ability to purchase reagents from a single supplier additionally provides enormous benefits for standardizing workflows between locations. Together, these components help create a more defined and consistent LC-MS/MS adoption pathway for clinical labs, reducing the technical complexity of mass spectrometry implementation.

Automation drives speed and scale

The same innovations that simplify implementation also enable automation of mass spectrometry workflows. When manual LC-MS/MS workflows were analyzed across six different analyte categories, they were shown to have a median completion time of 26 hours, with roughly one and a half hours of hands-on time.³ However, in some cases, LC-MS/MS workflows exceeded 72 hours with over four hours of hands-on time.³ These lengthy timelines can be difficult to manage in clinical settings. Batch restrictions can further delay turnaround times, as labs hold samples to ensure that assays are run with full batch volumes to maximize the efficiency of this arduous analytical technique.

Automated, random-access mass spectrometry systems address these pain points. In the same multi-lab study of six analyte categories, automated LC-MS/MS workflows had a median run time of two hours and required only five to fifteen minutes of hands-on time.³ These gains are not only important for turnaround time, but also for capacity. With automated workflows, staff are free to oversee other testing while spending less time on repetitive MS sample preparation or technically demanding analysis steps. Random-access further contributes to increased capacity, allowing samples to enter the workflow as they arrive, ensuring patients and care teams receive results as efficiently as possible.

However, in order for automated workflows to be scalable, labs must have an efficient way to review data. Mass spectrometry results can be particularly time-consuming to review, as each analyte can generate several “peaks”, and each peak must be assessed on multiple criteria, including retention time, signal-to-noise ratio, peak height, and more. Algorithms can help streamline data review, using defined parameters to rapidly classify acceptable results and flag questionable data for expert review. This helps keep human judgment focused where it adds the most value and equips clinical labs with the tools they need to handle increased mass spectrometry volume.

Together, these technological advances make LC-MS/MS more compatible with the demands of clinical laboratories. Standardized reagents, cartridges, calibration, and data review also improve transferability between laboratories. When sites use comparable workflows, training is easier to replicate, results are more consistent, and multi-site studies become more reliable. Automated mass spectrometry systems make LC-MS/MS a scalable analytical practice, encouraging more labs to adopt this powerful technique.

The next phase of mass spectrometry

As the ability to implement and scale mass spectrometry improves, the potential applications of mass spectrometry will expand. Established uses are likely to grow first. Endocrinology will benefit from an increased ability to measure steroid hormones with a degree of specificity and sensitivity that immunoassays may lack.¹ LC-MS/MS is also frequently beneficial for therapeutic drug monitoring, which allows care teams to optimize individual dosing regimens or monitor compounds with variable pharmacokinetics.⁴ Toxicology and metabolite analysis will similarly benefit from the increased accessibility of LC-MS/MS, which can detect challenging molecules at low concentrations.

Yet many opportunities have yet to be fully explored. As LC-MS/MS technology becomes more accessible and as throughput capacity increases, clinical laboratories can begin evaluating new uses for LC-MS/MS. This could include more routine use in newborn screenings, expanding into new analyte categories, and bringing the benefits of LC-MS/MS to smaller or more remote patient populations.

Mass spectrometry is reaching an inflection point. Its next phase will be shaped less by the analytical principle—which is already well established—than by the technologies surrounding it. By simplifying protocols, reducing turnaround time, and improving data review, emerging systems make LC-MS/MS easier to implement and more practical to scale. This operational transformation should ultimately broaden access to this important analytical tool and unlock the next generation of clinical mass spectrometry applications.

Author Bio

Allyson Kozak, PhD, MBA, NRCC, is senior scientific affairs manager for Mass Spectrometry and Women’s Health at Roche Diagnostics. She leads medical strategy focused on advancing diagnostic solutions that support timely and informed clinical decision-making. With more than 15 years in clinical laboratory science and analytical chemistry, Kozak brings deep expertise in advancing diagnostic innovation and laboratory practice. She works closely with key opinion leaders to align innovation with real-world clinical needs, generate robust evidence across the product lifecycle, and support healthcare decision-makers in improving patient outcomes.

Kozak holds a PhD in chemistry from Ohio University, where her research focused on nitric oxide and oxidative stress in cardiac preservation, as well as an MBA in finance. She also earned a BA in chemistry from The College of Wooster and is certified by the National Registry of Certified Chemists (NRCC).

References

1. French D. Clinical utility of laboratory-developed mass spectrometry assays for steroid hormone testing. Journal of Mass Spectrometry and Advances in the Clinical Lab. 2023;28:13-19. doi:10.1016/j.jmsacl.2023.01.006.

2. Recent Trends in the Use of LC-MS-MS for the Testing of Food and Environmental Contaminants | Spectroscopy Online. 2026. Accessed April 22, 2026. https://www.spectroscopyonline.com/view/recent-trends-use-lc-ms-ms-testing-food-and-environmental-contaminants

3. Vermeersch P, de Jonge R, Miyazawa T, et al. Comparison of six serum analyte workflows using routine liquid chromatography-tandem mass spectrometry methods at multiple laboratories with the cobas i 601 analyzer, an automated mass spectrometry system. Clinical Chemistry and Laboratory Medicine. Published online January 26, 2026. doi:10.1515/cclm-2025-0994.

4. Kang JS, Lee MH. Overview of therapeutic drug monitoring. Korean Journal of Internal Medicine. 2009;24(1):1. doi:10.3904/kjim.2009.24.1.1.