The Expanding Role of Mass Spectrometry at the Cutting Edge of Research
From diagnosing disease to analyzing Martian soil, mass spectrometry is powering breakthroughs across science with unmatched molecular precision.
With its unmatched precision in identifying and quantifying chemical compounds, mass spectrometry has a vast range of applications across virtually every field of scientific research.
Mass spectrometry is a common analytical technique used to identify and quantify molecules in a sample. It works by turning a sample's molecules into electrically charged ions. A mass spectrometer then precisely measures the mass-to-charge (m/z) ratio of ions and ion fragments to produce a detailed molecular fingerprint.
“Although the technology is complex, in many ways the concept is quite simple,” said James McCullagh, a professor of biological chemistry and director of the Mass Spectrometry Research Facility at the University of Oxford. “You’re precisely measuring the mass of small molecules to determine which elements are present and in what proportions – this reveals their chemical formula.”
Thanks to its high sensitivity, specificity and versatility, mass spectrometry is central to a wide range of applications – from biomedical research, drug discovery and development, clinical diagnostics and environmental analysis.
“It allows you to profile compounds in complex mixtures – such as air, soil or water, and biological samples,” said Mark Fitzsimons, a professor of environmental chemistry at the University of Plymouth.
As the technology continues to evolve, delivering higher resolution, faster data acquisition and advanced imaging capabilities, it is opening new frontiers in both scientific discovery and real-world applications.
Mass spectrometry: Powering biomedical research
Mass spectrometry has become an essential tool in biomedical research, offering unparalleled precision in identifying, quantifying and characterizing a broad spectrum of biomolecules – including proteins, peptides, lipids and metabolites – in biological samples like cells, tissues and biofluids.
“We’re using mass spectrometry to understand what’s happening at the molecular level – to unravel the complex mechanisms that underpin health and disease,” explained McCullagh.
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In proteomics, mass spectrometry enables high-throughput protein profiling, protein-protein interaction studies and the detection of post-translational modifications. In metabolomics and lipidomics, it supports the analysis of thousands of small molecules and lipid species, providing insights into metabolic and signaling pathways central to physiology and pathology.
“The next step is multiomics – integrating the different types of molecular data to gain a systems-level view,” said McCullagh.
Recent advances in mass spectrometry technologies are opening new frontiers. Mass spectrometry imaging (MSI), for instance, allows the direct analysis of solid samples by scanning across a surface to generate detailed molecular maps.
“MSI is a very powerful tool,” says McCullagh. “Unlike traditional approaches that require sample homogenization and extraction, it enables visualization of the spatial distribution of molecules within a sample, such as a tissue section.”
Recent advances in technology have significantly improved spatial resolution and acquisition speed, allowing researchers to capture high-definition snapsnots of molecular distributions. State-of-the-art single-cell MSI now allows precise localization of molecules within individual cells – offering a powerful, spatially resolved layer of information that extends beyond the capabilities of conventional omics approaches.
Mass spectrometry: From bench to bedside
Mass spectrometry has a variety of applications in translational research, from accelerating drug discovery and development to enhancing diagnostics and enabling more personalized treatment strategies.
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In early-phase drug discovery, advancements in instrumentation and automation have transformed mass spectrometry into a powerful tool for high-throughput screening of vast libraries of chemical compounds with speed and precision. As drug candidates progress through preclinical and clinical development, the technique becomes essential for drug metabolism and pharmacokinetics (DMPK) studies – providing insight into how a drug is absorbed, distributed, metabolized and excreted. These data are critical for optimizing dose, improving bioavailability and ensuring safety and efficacy.
Mass spectrometry is also embedded into clinical diagnostic laboratories where it is used for newborn screening for metabolic disorders, therapeutic drug monitoring and clinical toxicology. Its ability to generate detailed molecular profiles also makes it a key tool in precision medicine research, helping identify biomarkers for earlier diagnosis and personalized treatments.
“If you give the same drug to a hundred different people, they will each respond differently due to genetic variation within the group – this diversity personalizes both efficacy and side effects,” said McCullagh. “One size does not fit all; we need to understand and work with those personalized effects to improve diagnosis and treatment strategies.”
Recent innovations have further expanded the potential clinical utility of the technique. For example, ambient ionization mass spectrometry allows the direct analysis of biological samples – such as blood, urine, tissue, saliva, sweat skin and even exhaled breath – with little or no sample preparation. This opens up exciting possibilities for point-of-care and personalized diagnostics, where rapid, on-site molecular analysis could support timely clinical decisions.
A striking example is the intelligent knife (iKnife), an innovative surgical tool that combines electrosurgery and rapid evaporative ionization mass spectrometry (REIMS). By providing tissue analysis during surgery, this promising device helps to distinguish between healthy and cancerous tissues in real-time, helping guide surgery and potentially leading to improved outcomes.
Mass spectrometry: Environmental analysis
Mass spectrometry plays a vital role in environmental science, offering the precision and sensitivity required to detect, identify and quantify pollutants across a wide range of environmental samples. By monitoring exposure to potentially hazardous substances, scientists can assess risks to human health and ecosystems with greater accuracy.
“Its ability to analyze complex mixtures at high sensitivity makes it ideally suited for studying air, water or soil samples, where contaminants often occur at extremely low concentrations,” explained Fitzsimons.
In air quality research, mass spectrometry is widely used to monitor airborne pollutants, such as volatile organic compounds (VOCs) particulate matter, or greenhouse gases. Proton-transfer-reaction mass spectrometry (PTR-MS), for instance, enables real-time, sensitive and quantitative analysis of VOCs in the atmosphere.
“A major advantage of PTR-MS is that samples don’t need preparation before measurement,” says Fitzsimons.
Mass spectrometry is equally valuable in soil analysis, where it supports studies of elemental and organic composition, as well as gaseous emissions. These capabilities are essential for assessing soil health, tracking pollutants and understanding the mobility and persistence of contaminants. “Mass spectrometers have even been used to analyze Martian soil,” noted Fitzsimons, highlighting the technique’s extraordinary
versatility.
Water monitoring is another key area, particularly in the detection of emerging contaminants in wastewater and surface waters. Pharmaceuticals, for instance, can enter aquatic ecosystems through industrial discharges or hospital effluents, raising concerns about long-term environmental and human health impacts. “We know the structure of these molecules, so mass spectrometry is a perfect tool for their analysis,” said Fitzsimons.
Mass spectrometry is also widely used to detect persistent organic pollutants (POPs) and their metabolites in diverse samples, from drinking water to biofluids. These synthetic chemicals are of global concern due to their extreme resistance to degradation, ability to bioaccumulate and potential long-term health effects.
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“There is important research ongoing to identify the accumulation of POPs in the biosphere and associated risks from exposure to these long-lived pollutants,” said McCullagh. “Large-scale epidemiology studies are very much driven by the incredible sensitivity of mass spectrometry, which allows researchers to detect these compounds in blood or other samples at trace levels.”
For example, recent research has linked exposure to perfluoroalkyl substances (PFAS) in the womb with an increased risk of developing type 1 diabetes.
Mass spectrometry: Far-reaching applications
Wherever there is a need to identify and quantify chemical compounds with precision, mass spectrometry has become an indispensable tool.
“Mass spectrometry has given us this enormous capacity to ask and answer important questions,” said Fitzsimons. “It’s the spectrum of possibilities that makes it so exciting.”
While mass spectrometry is firmly established in biomedical and environmental research, its reach extends far beyond these fields. In forensic science, it plays a vital role in many areas including drug testing, toxicology, and the analysis of trace evidence such as explosives or unidentified substances. Archaeologists use it to study ancient materials, providing insights into past human activity and the environment. In the food and agriculture industries, mass spectrometry helps ensure product safety and quality by detecting contaminants, verifying authenticity, and analyzing nutritional content.
“You’d be hard pushed to find a scientific discipline that does not utilize mass spectrometry in some way,” said McCullagh. “I often say it’s used ‘from archaeology to zoology’ – and this is literally the case.”
