Global food systems continually grapple with the critical challenge of safeguarding against naturally occurring toxins. In particular, mycotoxins from fungi and tropane alkaloids from plants pose an ongoing threat to global food security and trade. Detecting and quantifying these toxins requires analytical techniques that can effectively manage complex matrices, ultra-trace levels, and evolving regulatory standards.
Holly Lee, Staff Scientist at SCIEX, has been at the forefront of developing and communicating new strategies for tackling these analytical challenges. Drawing on her recent presentation at the 2025 North American Chemical Residues Workshop (NACRW), Lee discusses how next-generation quantitation tools and workflows are transforming the detection of natural toxins in food.
Complex Analytes, Emerging Challenges
“The quantitation of mycotoxins and tropane alkaloids is challenged by the diversity of analytes, the presence of interferences in complex food matrices, and the stringent method performance required to comply with regulatory acceptance criteria,” explains Lee.
She adds that new environmental and agricultural factors are intensifying the issue. “Beyond climate-related factors that have led to the increase in co-occurring mycotoxins in new regions and food commodities, the emergence of masked mycotoxins presents a new challenge due to their ability to evade conventional analytical detection methods.”
These analytical obstacles underscore why liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) remains the technique of choice for analysts. “It’s considered a gold standard due to its high specificity, sensitivity, and ability to simultaneously detect multiple analytes,” says Lee.
Regulation Driving Sensitivity Demands
Global regulations continue to tighten, prompting laboratories to push the limits of sensitivity and reproducibility. “Mycotoxin levels are regulated globally through national legislation and international agreements among countries,” Lee notes. “The European Commission, for example, established maximum levels (MLs) as the highest legally tolerated levels of specific contaminants in food and feed when good agricultural practices are followed.”
Current EU MLs for regulated mycotoxins in most food commodities range from tens to hundreds of micrograms per kilogram (μg/kg). Baby food matrices, however, are subject to much lower limits, often in the sub-to-low μg/kg range.
Recent updates to Regulation (EU) 2023/915 have further tightened requirements by lowering MLs for key Fusarium toxins such as deoxynivalenol (DON), and introducing new limits for DON and T-2/HT-2 toxins in specific food products. “These changes require pushing sensitivity limits further for low-level quantitation in both existing and emerging matrices,” Lee explains.
Hardware and Software: A Dual Frontier of Innovation
New developments in both instrumentation and workflow management are transforming the way scientists approach toxin quantitation. Lee points to advancements in triple quadrupole technology, such as the SCIEX 7500+ system, as an example of how instrumentation and workflow design are evolving in tandem.
“The overall performance of any analytical method is influenced by the quality measures implemented throughout the entire workflow,” she explains. “Good chromatographic method development is critical for ensuring that structurally similar toxins are adequately resolved from one another and from interferences.”
Hardware innovations further enhance robustness. “The SCIEX 7500+ system incorporates Mass Guard technology to minimize downstream contamination of critical ion path components, maintaining optimal sensitivity over thousands of injections of complex food extracts,” observes Lee. “The inclusion of removable front-end components also provides greater flexibility for scheduling cleaning, improving both instrument uptime and lab efficiency.”
The SCIEX 7500+ system also supports ultrafast multiple-reaction-monitoring (MRM) acquisition, capturing hundreds of transitions per cycle. “Large-panel quantitative screening is typically limited by the compromise between the size of the target list and the resulting data quality,” asserts Lee. “The ultrafast MRM acquisition delivers accurate and precise quantitation of panels comprising hundreds to thousands of analytes.”
Addressing Matrix Effects with MS Technology
Matrix effects can hinder quantitation by suppressing or enhancing signals. According to Lee, mass spectrometers that support advanced workflows—such as SCIEX systems with linear ion trap (LIT) capability—can help address these challenges. Workflows, such as MRM3 scans, provide enhanced specificity. “In an MRM3 scan, the dual fragmentation of analyte precursor ions produces second-generation product ions, yielding more unique and compound-specific transitions than conventional MRM,” Lee says. “This is especially useful for distinguishing co-eluting compounds and removing matrix interferences.”
These capabilities have proven particularly valuable for ultra-trace analysis. “Leveraging the ultrafast-scanning SCIEX 7500+ system, MRM3 scans can be acquired in parallel with a full mycotoxin MRM screen without a significant increase in cycle time,” Lee adds. “We’ve demonstrated this approach for aflatoxins in baby food and plant-based meat.”
Toward Smarter, Greener, and Automated Workflows
Looking ahead, Lee sees three defining themes for next-generation quantitation:
- Automation: Focusing on automated sample preparation technologies, such as automated solid-phase extraction (SPE).
- Miniaturization and green chemistry: Implementing techniques such as micro-SPE for reducing solvent waste and improving sustainability.
- Artificial intelligence (AI): Using AI to remove the burden of data processing from laboratory personnel, freeing up valuable scientist time.
Future method development, she adds, should focus on incorporating these technologies “to improve existing methods—reducing sample volume and waste—while ensuring data quality remains compliant with regulated protocols.”
Empowering Scientists Through Software
Lee emphasizes that advances in software can be just as transformative as hardware upgrades. “Be creative with what you have at your disposal in your toolbox,” she advises. “While instrument performance is tied to the model and its hardware features, numerous software features—often overlooked—can help improve acquisition workflows and lab efficiency.”
Lee points to SCIEX OS software, available on both nominal and accurate mass platforms, as an example. “It features automated workflows for batch and queue management, compound optimization, and data processing,” she says. “All of these can be streamlined for minimal user intervention to boost operational efficiency in routine laboratories.”
A Holistic Future for Food Safety Analysis
For Lee, the direction of the field is clear: greater automation, higher throughput, and smarter, greener workflows. “All of the above,” she says. “The industry is moving toward solutions that make labs not only more efficient but also more sustainable and resilient.”
As laboratories worldwide seek to keep pace with evolving regulatory demands and global food safety challenges, Lee’s message to her peers remains simple: “Be creative, and use every tool available to you. That’s where the next generation of quantitation begins.”