Emerging Trends and Challenges in Detecting Residues and Contaminants in Food in the Exposome Era

Hernández-Mesa,Maykel;Dervilly,Gaud;Le Bizec,Bruno;Ana M. García-Campaña;

Key Points:

By integrating biomarkers of exposure, effect, and susceptibility, exposomics enables a mechanistic understanding of how complex chemical mixtures—often at individually "safe" levels—interact to influence chronic disease risk.
Emerging "mega-methods" like QuEChERSER and sustainable solvents, along with cutting-edge instrumentation such as LC–IMS–MS, GC–HRMS, and CE–HRMS, are essential to broaden analytical coverage and enhance detection capabilities across the external exposome.
Standardized workflows, interoperable data, and integrated interpretation strategies are crucial for translating complex exposomic data into actionable public health insights and regulatory interventions.

Chemical exposomics connects lifetime exposure to chemicals with environmental disease risk, offering valuable insights for health prevention and identifying food as a major exposure source. Profiling food chemically helps detect co-exposures, define aggregated exposure pathways, and improve risk assessments. Yet identifying many chemical classes in complex food remains difficult. High-throughput “mega-methods” using advanced techniques and efficient sample preparation are needed. Combining platforms such as liquid chromatography–high-resolution mass spectrometry (LC–HRMS), gas chromatography–HRMS (GC–HRMS), both with ion mobility spectrometry (IMS), and capillary electrophoresis–HRMS (CE–HRMS) supports broad suspect screening and non-targeted analysis in food exposomics.

Throughout our lives, we are exposed to numerous chemical agents found in the environment—originating from industrial, agricultural, and livestock activities—as well as through food. The risk of developing chronic diseases is influenced by both genetic and environmental factors and their interactions. From a public health perspective, understanding chemical exposure levels, associated risks, and the mode of action (MoA) of these substances is essential for implementing effective disease prevention strategies.

Chemical risk assessment remains a significant challenge because of the vast number of potentially hazardous compounds in circulation—approximately 140, 000 chemical substances registered for use in Europe and around 86,000 in the United States (1). While chemical exposures may result from environmental, occupational, or lifestyle sources (smoking, alcohol consumption), food is considered the primary route of exposure to harmful chemicals. The European Food Safety Authority (EFSA) has identified approximately 4750 chemicals in food with potential health risks (2). For most of these substances, there are limited data regarding distribution, toxicity at realistic exposure levels, or their behavior in chemical mixtures typically encountered in everyday life (3).

There is a growing interest in understanding the health effects associated with chemical mixtures, shifting away from traditional toxicological and epidemiological approaches. Toxicology has historically evaluated single chemicals, often ignoring the interactive effects found in real-world exposure scenarios—such as potentiation, synergy, and antagonism—and typically assuming additive effects only (4). For this reason, exposure to mixtures of chemical substances could lead to significant toxicity, even if all components are present at concentrations that are individually considered “safe” (based on acceptable or tolerable daily intakes). As a consequence, modern epidemiology is evolving to explore the consequences of chemical mixtures without predefined hypotheses, representing a more holistic and data-driven approach to risk assessment (5).

The emerging field of “exposomics” is based on the hypothesis that environmental factors can induce physiological and molecular changes in organisms—such as metabolic disruptions, protein modifications, adductions and DNA mutations, epigenetic alterations, and/or alterations in the microbiome—each of which may have negative health consequences (3,6). A core goal of exposomics is the identification of biomarkers that connect exposures to biological responses and health outcomes (7): biomarkers of exposure (exogenous substances, their metabolites or interactions reflecting exposure), biomarkers of effect (endogenous changes associated with early or ongoing health effects), and biomarkers of susceptibility (inherent or acquired capacity of an organism to respond to a given exposure).

Exposomicsaims to comprehensively identify all environmental exposures over a person’s lifetime and link these exposures to non-genetic diseases (8). This includes the characterization of both exogenous chemicals (biomarkers of exposure encompassing the exposome) and endogenous compounds generated or modified in response to environmental stressors (biomarkers of effect unveiled by omics approaches) (Figure 1). The exposome is commonly divided into two domains (9): the internal exposome, which involves the study of biomarkers of exposure in the individuals (for example, biofluid analysis); and the external exposome, which includes the characterization of chemical residues and contaminants in sources of exposuresuch as air, water, or food.

While many exposomics studies have traditionally focused on internal biological measurements, there is growing recognition of the value of characterizing the external exposome—particularly through its connection to the aggregated exposure pathway (AEP), which outlines the sequence from a chemical source such as food to its biological site of action, representing the initiating molecular event in an adverse outcome pathway (AOP). AOPs then trace the cascade of biological events leading to observable health effects, thus providing a mechanistic link between exposure and disease. Integrating exposome data into AEP/AOP frameworks enhances the capacity to predict adverse outcomes and understand the roles of chemical mixtures and multiple exposure routes (10).

In this sense, exposomics requires integrated approaches that connect sources of exposure with affected individuals, by means of three complementary strategies (11,12):

Top-down approaches: These focus on biological samples (blood, urine, placenta) to capture internal exposure and biological effects. Unlike traditional biomonitoring, this approach is not limited to predefined chemicals, aiming instead to detect a broad spectrum of exposures. Environment-wide association studies (EWAs) are central to this strategy, linking multiple exposure biomarkers with biological responses (13). This approach also helps identify chemicals with different structures but similar health effects because of shared MoAs.

Bottom-up approaches: These start from environmental or food sources and trace contaminants through ecosystems into the human body. They emphasize source attribution, pathway modeling, and mixture characterization. These approaches are important for monitoring chemical residues in air, water, soil, and food, and for identifying exposure hotspots to inform regulation and intervention.

“Meet-in-the-middle” approaches: These integrate the top-down and bottom-up methodologies by identifying intermediate molecular biomarkers associated with both exposures and outcomes. These biomarkers reflect both exposure and effect, thereby improving causal inference and supporting the validation of exposure-disease associations. This strategy aligns mechanistic insights with observed public health trends, enhancing the detection of early warning signals and aiding the prioritization of preventive actions.

These strategies are complementary and synergistic: top-down strategies reveal internal exposure and biological response patterns; bottom-up approaches trace the sources and pathways of exposure; and “meet-in-the-middle” approaches provide mechanistic validation of causality. They offer a systems-level understanding of how environmental chemicals impact health over time, and more importantly, underscore the relevance of investigating food products within the exposomics framework.

Despite recent advances, exposomics relies on robust analytical methods capable of detecting and quantifying a wide variety of chemicals with different physicochemical properties across diverse sample types (14). In the context of food safety, studying the external exposome requires techniques that can simultaneously detect multiple classes of residues and contaminants associated with adverse health outcomes. Therefore, significant efforts must focus on developing comprehensive “mega-methods” that can quantify a wide range of chemicals in a single run (15,16), improving co-exposure risk assessments and enabling source identification.

Food as an Exposure Source: Analytical Challenges and Advances

This is a critical step in exposomics, particularly when analyzing complex food matrices that may contain a wide array of (un)known chemical residues and contaminants at trace levels. The broad polarity range and structural diversity of xenobiotics—such as pesticides, veterinary drugs, mycotoxins, phytotoxins, and plasticizers, among others—pose significant challenges to the use of a single, standardized extraction protocol. Consequently, the development of robust, versatile, and environmentally sustainable extraction techniques remains a key analytical priority. This challenge is further exacerbated by the intrinsic variability of food matrices, which can differ substantially in composition—from lipid-rich and protein-dense to fibrous or aqueous—often requiring matrix-specific strategies to ensure reliable analyte recovery and high-quality data.

Matrix effects represent another major concern in food analysis, particularly when using high-resolution mass spectrometry (HRMS). Co-extracted matrix constituents can lead to ion suppression or enhancement, thereby compromising sensitivity, accuracy, and overall analytical reliability. While strategies exist to mitigate matrix effects (17) (when complete elimination is not feasible), ongoing efforts continue to focus on optimizing sample preparation methods. Dilute-and-shoot approaches are often favored for their simplicity and potential for broad analyte coverage while reducing matrix effects (18); however, they may compromise sensitivity for compounds present at trace levels.

Conventional sample preparation methods such as liquid/solid–liquid extraction (LLE or SLE), solid-phase extraction (SPE), and the QuEChERS (Quick, Easy, Cheap, Effective, Rugged, and Safe) approach are widely used in the analysis of food as exposure source (14). Although SPE offers high performance in terms of analyte recovery and sample cleanup, it is typically optimized for specific chemical classes and may not support the broad-spectrum chemical detection required in exposomics. QuEChERS has proven to be a cost-effective and versatile approach for multiresidue determination, using different sorbents for sample cleanup—primarily primary secondary amine (PSA), octadecylsilane (C18), graphitized carbon black (GCB), and zirconium dioxide-based sorbent and derivatives, as well as diatomaceous earth or enhanced matrix-removal-lipid materials (19). However, the QuEChERS approach may also fall short in covering analytes with a wide polarity range in a single analysis (16). Lehotay et al. have recently proposed an updated version referred as QuEChERSER (Quick, Easy, Cheap, Effective, Rugged, Safe, Efficient, and Robust) mega-method, which reduces the number of methods required to determine a broad scope of analytes. This approach extends analyte coverage, enabling complementary determination of both liquid chromatography (LC)- and gas chromatography (GC)-amenable compounds. For instance, this QuEChERSER strategy has been successfully applied to the determination of 245 chemicals (211 pesticides, 10 polychlorinated biphenyls [PCBs], five polybrominated diphenyl ethers [PCDEs], 16 polycyclic aromatic hydrocarbons [PAHs], and three tranquilizers) across 10 different food commodities, encompassing both non-fatty and fatty products (20). This approach has also been used for the determination of veterinary drugs (21).

A promising trend in sample preparation is the use of deep eutectic solvents (DESs), particularly natural deep eutectic solvents (NADESs), which are gaining attention for their sustainability and compatibility with high-throughput workflows—features increasingly valued in food analysis and exposome-based studies. NADESs are typically formed by mixing a hydrogen-bond acceptor (HBA) with a hydrogen-bond donor (HBD), often derived from natural compounds such as organic acids, sugars, alcohols, or choline derivatives (22). These mixtures are biodegradable, non-toxic, and offer tunable extraction properties through adjustments in component ratios, temperature, or water content. Their unique physicochemical features, such as customizable polarity, enable the extraction of a broad spectrum of analytes, making them particularly well-suited for the complex chemical diversity encountered in food exposomics. While the applicability of NADESs has been successfully demonstrated in various food safety contexts (23), their full integration into exposomics workflows remains under development. Nevertheless, their potential for broad analyte coverage, as demonstrated in metabolomics studies (24), and their alignment with green chemistry principles, position them as a valuable tool for future sample preparation strategies in the field.

High-performance analytical methods are essential for exposome studies. Although early advances in exposomics have provided insights into relevant chemical mixtures in food—considered part of the external exposome—this raises the question of whether all such hazardous chemical mixtures can be analyzed simultaneously in complex food matrices. Over the past decades, substantial research has addressed the targeted determination of specific chemical residues and contaminants in food and their associated health impacts (25). While targeted LC–HRMS methods are capable of detecting up to 1200 compounds (26)—including biotoxins, pesticides, and veterinary drugs—in complex food-related matrices, comprehensive characterization of chemical hazards remains challenging. In this context, suspect screening and non-targeted methods have emerged as key strategies for the holistic detection of biomarkers of exposure in the external exposome, mirroring their successful application in internal exposome research (27).

Suspect screening and non-targeted methods enable comprehensive data analysis, including retrospective evaluations, to identify biomarkers of exposure, trace exposure sources, and detect unexpected chemical hazards in food—insights often missed by conventional targeted approaches. The primary advantage lies in the ability to detect a wide range of chemicals with diverse physicochemical properties. However, their application to the external exposome presents several critical challenges: i) their performance is highly dependent on the nature of the chemical compounds under investigation; ii) quantification of chemical substances can be cumbersome and may not yield accurate hazard-level assessments at sources of exposure; iii) many xenobiotics occur at trace levels in food, making their detection difficult in complex matrices; iv) analytical standards for all exposure biomarkers are not readily available in laboratories, necessitating alternative strategies for unequivocal identification; v) unknown chemical hazards with significant health impacts require new analytical tools for their detection.

The development of HRMS techniques such as time-of-flight mass spectrometry (TOF-MS) and orbital trap MS has significantly expanded analytical capabilities, shifting the focus from targeted analysis of a limited number of compounds to a more comprehensive assessment of chemical hazards in food. LC coupled to HRMS—and to a lesser extent GC–HRMS—has become the main analytical platform for suspect screening and non-targeted analysis of xenobiotics in food. Nonetheless, limitations persist. For instance, the identification of isomeric and isobaric xenobiotics remains challenging with LC–HRMS or GC–HRMS.

Ion mobility spectrometry-mass spectrometry (IMS-MS) has gained interest as acutting-edge technology capable of distinguishing molecules based on their gas-phase conformation (28). IMS-MS enables the rapid separation (within milliseconds) of isobaric and isomeric species in a neutral drift gas (N₂) under the influence of an electric field, according to their mass-to-charge ratio (m/z) and shape (expressed as collisional cross-section, CCS). By introducing an additional dimension of separation to LC–HRMS workflows, IMS enhances the resolution of matrix components and chemical artefacts from analytes of interest, facilitating their detection even at low abundance. Moreover, various IMS-MS technologies—such as drift tube ion mobility spectrometry (DTIMS), traveling wave ion mobility spectrometry (TWIMS), and trapped ion mobility spectrometry (TIMS)—allow for CCS measurements that provide complementary information to retention indices and mass spectra in molecular identification efforts (29).

The potential of IMS-MS to overcome analytical challenges in molecular identification—still the primary bottleneck in non-targeted analysis—is increasingly recognized in many research fields (30,31). Recent applications in food analysis have demonstrated its value in detecting chemical hazards, thereby enhancing our understanding of the external exposome (32,33). However, further research is needed to evaluate the extent to which integrating IMS into LC–HRMS workflows improves the deconvolution of complex chemical mixtures in food (25). In parallel, progress is required in the standardization and implementation of CCS as a robust identification parameter. Although several CCS databases for small molecules, including xenobiotics, have been developed (34,35)—and considerable efforts are underway to use CCS data in exposomics interpretation (36)—only a limited fraction of health-relevant chemical hazards have been characterized in terms of CCS. Moreover, the reliability of transferring CCS data across laboratories using different IMS technologies remains uncertain, largely due to the limited number of interlaboratory studies (29,37,38). Thus, the standardization of LC–IMS-MS workflows—including calibration procedures and data analysis protocols—and the development of high-quality reference CCS databases are, among others, critical goals to ensure the successful adoption of this technology in analytical laboratories and its effective implementation in food analysis and exposomics-related research (39).

Based on the above considerations, integrating complementary analytical techniques alongside traditional methods is essential to advance the field of exposomics. Although LC–IMS-MS in combination with GC–IMS-MS workflows can provide a broad overview of chemical hazards in this exposure source, capillary electrophoresis (CE)–HRMS is also needed to complete the picture by enabling the determination of highly polar and charged analytes that are not adequately covered by hydrophilic interaction liquid chromatography (HILIC) (14,40), providing complementary insights into the polar fraction of sample analyses (41).

Conclusions

Exposomics has emerged as a powerful framework for understanding the links between environmental exposures and human health, creating new opportunities for analytical chemists. Their role is crucial in developing advanced methods for the comprehensive detection of biomarkers and chemical hazards across both the internal and external exposome. In particular, investigating food as a source of exposure highlights the shift from targeted to suspect screening and non-targeted analyses in the food safety field. However, this also presents major challenges, such as detecting low-abundance xenobiotics in complex food matrices or confidently identifying unknown compounds, among others. A current trend is the development of high-throughput, sustainable “mega-methods” capable of covering a wide range of analytes with diverse physicochemical properties. Exposome studies increasingly require collaboration among experts in LC–HRMS, GC–HRMS, IMS-MS, and CE–HRMS, as only the combination of these complementary techniques can fully expand the analytical window and enable holistic chemical characterization. Accordingly, chemical analysts must deliver high-quality data to support exposome-based findings, making harmonization and standardization of high-performance methods a critical objective. However, analytical performance alone is not enough. Effective integration and interpretation of complex data sets are also essential, highlighting the need for analytical chemists to collaborate with data scientists, bioinformaticians, toxicologists, and epidemiologists in multidisciplinary teams. Their expertise is key to advancing exposomics—from method development to data interpretation—ultimately enhancing exposure assessments and supporting better public health decisions.

Acknowledgments

MHM gratefully acknowledges the grant RYC2023-044255-I funded by MCIU/AEI/10.13039/501100011033 and ESF+. This work was also supported by Grant CNS2024-154893 funded by MICIU/AEI/10.13039/501100011033.

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Maykel Hernández-Mesa is a Ramón y Cajal researcher at the University of Granada (Spain). His work focuses on characterizing the external and internal exposome, with particular interest in the determination of pesticides, mycotoxins, and plant toxins, and in expanding analyte coverage through ion mobility–mass spectrometry and capillary electrophoresis–mass spectrometry.

Gaud Dervilly is a public health researcher and deputy director of the LABERCA research unit at Oniris in Nantes (France). With over 20 years of experience, her work focuses on consumer exposure to chemical hazards—including environmental contaminants—and their potential impacts on human health. Membership in scientific councils both at institutional levels (National Veterinary College, Nantes) and at international scientific event (Euroresidue, NL; ISEAC, NL; International Food and Water Research Center, Singapore).

Bruno Le Bizec is a professor at Oniris VetAgroBio, Nantes (France) and director of LABERCA, a research unit focusing on the characterization of the human chemical exposome. Very early on, Bruno and his team developed mixed approaches aimed at characterizing the external and internal markers of chronic exposure to chemical contaminants in humans, and using a metabolomic approach to investigate the markers of effect resulting from this exposure, with a view to studying the link between dietary exposure to chemical hazards and health diseases.

Ana M. García-Campaña is a professor at the University of Granada, responsible for the team “Quality in Food, Environmental and Clinical Analytical Chemistry” (FQM-302). Her research areas are focused on the use of advanced analytical platforms based on liquid chromatography and capillary electrophoresis coupled with mass spectrometry, fluorescence, or ion mobility spectrometry for food and environmental quality control and safety, monitoring contaminants, including natural toxins and residues of veterinary and human drugs and pesticides, including external and internal exposome studies. She is currently vice-president of the Spanish Society of Chromatography and Related Techniques (SECyTA).