The expansive use of pesticides in the 20th century, along with fertilisers, revolutionised and stabilised global food production, and dramatically reduced global famine rates. In addition to improving productivity by minimising crop losses and yield reduction, pesticides have helped increase the quality of food around the world.
However, the use of pesticides in food must be controlled to align with regulations. International efforts, like the World Health Organization (WHO) pesticide initiative,1 aim to protect food consumers from misuse of pesticides and maintain food product integrity by ensuring accurate labelling of foods. Monitoring pesticide levels is a key part of these initiatives. For example, the analysis of produce labelled as organic is required to detect any use of synthetic pesticides. Regulatory groups, like the European Commission, set maximum residue levels (MRL) for pesticides in different food products of plant and animal origin, to provide testing laboratories with set thresholds. These levels are often at low parts per billion (μg/kg).2
To meet these regulations, food testing laboratories need analytical systems capable of targeted and in some cases non-targeted analysis. Targeted analysis is important for detecting set lists of pesticides, which are specifically defined under regulations, while non-targeted analysis can rapidly expand the scope of the laboratories, facilitating false negative detections. The latter is particularly important in method development laboratories and for rooting out unexpected deliberate or unintentional misuse of pesticides, while also allowing retrospective analysis.
Although food testing laboratories have the analytical setup to monitor the defined pesticides of interest, many cannot easily perform untargeted analysis, so could miss new or misused contaminants. Here, we discuss how high-resolution mass spectrometry (HRMS) is overcoming these hurdles.
Detecting pesticides with mass spectrometry
With evolving regulations, food safety laboratories must ensure they are using optimal instrumentation to detect low concentrations of a large number of pesticides in complex matrices. Current routine methods for pesticide measurements are typically based on triple quadrupole mass spectrometry. These systems are designed to give ultra‑detailed analyses of a selected group of compounds in samples, meaning they are optimised for detecting selected pesticides in food samples that laboratories would expect to potentially find in such products.
However, triple quadrupole‑based methods are not designed to screen all components in a sample and, therefore, are limited in their ability to detect large numbers of non-targeted, unknown compounds.

HRMS helped to minimise interference in samples with more complex matrices, like orange and onion.
One solution is HRMS, a technique that complements triple-quadrupole mass spectrometry with its ability to identify and quantify large numbers of non-targeted pesticide compounds in food products, with the sensitivity required to meet regulations. Previously, HRMS had been considered complicated by some users with potentially overwhelming acquisition choices. However, new systems are designed for ease of use, with users able to select pre-designed method templates to suit their experimental needs. For example, drag and drop methods can analyse for mycotoxins or sets of specific pesticides. For full flexibility these can be edited and optimised, or customised method protocols can be made from scratch.
A major benefit of HRMS is it enables scientists to gain an overall view of all compounds in a sample. This is particularly advantageous when food laboratories cannot predict all potential contaminants, such as when analysing samples for food fraud, or detecting food contaminants and their metabolites. Global food chains are becoming increasingly complex, so the ability to scan food on a broader basis rather than just against a set list can be helpful to ensure no new contaminants escape detection. HRMS is also useful for complex samples as it can more easily distinguish between co-eluting peaks, minimising matrix interference.
The capabilities of HRMS in food testing
A recent paper aimed to understand the capabilities of the new high-resolution Thermo Scientific Orbitrap Exploris 240 MS in testing pesticides in food products. The researchers measured the levels of 244 pesticides in four sample types (tomato, onion, avocado and orange) using several different acquisition modes3 to determine the effectiveness of HRMS in detecting pesticides. In all samples, HRMS was able to detect all analytes at concentrations within European Commission MRLs and without any false positives. Moreover, HRMS helped minimise interference in samples with more complex matrices, like orange and onion.
The researchers also screened for non-target compounds to test the capability of the HRMS instrument in this setting. Mass spectral data was collected and evaluated against a group of over 900 compounds present in the EFS HRMS compound database and spectral library to identify any potential pesticides or their metabolites. In some cases, a metabolite of interest was detected where the parent compound had already disappeared. This showed that untargeted screening methods can help reveal the application of pesticides that are missed by a typical targeted approach, highlighting the benefit of untargeted screening.
Modernising pesticide use requires high resolution technologies
Pesticides are essential for stable food production, but it’s now up to global initiatives to maintain food product integrity and prevent misuse of pesticides. Food testing laboratories have an important role to play in this fight by providing a comprehensive analysis of food products to ensure they meet regulatory standards.
While triple quadrupole provides analysts with sufficient power and resolution for targeted analysis, there is a need for more comprehensive untargeted analysis within the industry. For this, HRMS is the ideal solution.
Ultimately, both HRMS and triple quadrupole systems are important for pesticide analysis in food samples. They improve the ability of food testing laboratories to detect existing and emerging pesticide contaminants to comply with evolving regulations. In order to meet ever-evolving regulations, food safety laboratories need the complementary powers of HRMS and triple quadrupole mass spectrometry systems.
Professor Amadeo R. Fernández-Alba
Amadeo has been Working Director of the European Union Reference Laboratory for Pesticide Residues in Fruits and Vegetables at the University of Almeria, Spain since 2006. He is a member of official organisations such as the Spanish Association for Standardization, the European Committee for Standardization (CEN), and is Vice President of the Evaluation of Education and Environmental Protection. He is also a member of the Committee of the Spanish Society of Mass Spectrometry and participates in the coordination of the Analytical Quality Control Guidelines, DG SANTE.
References
1. World Health Organization. Pesticide residudes in food. 19 February 2018. https://www.who.int/news-room/fact-sheets/detail/pesticide-residues-in-food
2. European Commission. EU Legislation on MRLs. https://ec.europa.eu/food/plant/pesticides/max_residue_levels/eu_rules_en
3. Rajski L, Petromelidou S, Díaz-Galiano FJ, et al. Improving the simultaneous target and non-target analysis LC-amenable pesticide residues using high speed Orbitrap mass spectrometry with combined multiple acquisition modes, Talanta. 2021. 228:122241.