Analytical Challenges for Pesticide Residue Analysis in Food: Sample Preparation, Processing, Extraction and Cleanup

Importance of the topic

Pesticide residues in food pose significant risks to consumer health and trade compliance. With over 1,600 registered active ingredients spanning diverse chemical classes (organophosphates, carbamates, pyrethroids, etc.) and various functional groups, laboratories must detect, quantify, and identify trace levels of residues across hundreds of commodity types. Achieving regulatory limits (maximum residue levels, MRLs) requires robust sample preparation, extraction, cleanup, and detection strategies to manage wide physicochemical diversity and matrix complexity.

Goals and overview

This white paper reviews the critical initial stages of pesticide residue analysis workflows in food matrices. Emphasis is placed on sample processing (comminution/homogenization), solvent-based extraction, cleanup techniques, and emerging reduced-scale and automated methods. The aim is to guide analysts in selecting and optimizing methods to balance accuracy, precision, speed, cost, and environmental considerations.

Methodology and instrumentation

Sample processing techniques:

• Room-temperature homogenization generates “soup” suspensions but risks enzymatic degradation, hydrolysis, and uneven analyte distribution.
• Cryogenic comminution with liquid nitrogen or dry ice produces flowable powders that preserve unstable residues and enhance homogeneity for small-scale extractions.

Extraction and cleanup approaches:

• QuEChERS acetonitrile extraction with salt partitioning and dispersive solid-phase extraction (dSPE) offers a fast, low-solvent, multi-residue workflow for GC-MS/MS and LC-MS/MS detection. Buffered (acetate or citrate) variants improve stability of base-sensitive pesticides.
• Reduced-scale organic solvent methods (acetone-based “mini-Luke,” ethyl acetate “SweEt”) and liquid/liquid partitioning deliver cleaner extracts for specific analyte classes or matrices with high starch, fat, or low water content.
• Single residue methods (QuPPe for polar/ionic pesticides, headspace for fumigants, acid digestion for dithiocarbamates) address compounds incompatible with generic multi-residue protocols.
• Automated accelerated solvent extraction (ASE) under elevated temperature and pressure accelerates analyte recovery from challenging matrices and integrates in-cell or in-line cleanup.

Instrument platforms include GC-MS/MS, GC-Orbitrap, LC-MS/MS, LC-Orbitrap, triple quadrupole systems, and supporting equipment such as dual-axis centrifuges and automated evaporators.

Main results and discussion

QuEChERS revolutionized routine multi-residue analysis by reducing sample and solvent volumes, simplifying workflows, and expanding analyte scope. However, matrix co-extractives, unstable pesticide losses, and incomplete cleanup necessitate complementary methods. Cryogenic processing minimizes degradation but demands specialized infrastructure. Alternative solvents and ASE improve extraction yields for polar, non-polar, or heat-labile compounds. Each technique involves trade-offs in throughput, cost, equipment, and regulatory validation.

Benefits and practical applications

• High throughput and reduced solvent use lower operating costs and environmental impact.
• Smaller sample sizes and miniaturized protocols enable rapid turnaround for monitoring and compliance.
• Modular workflows allow tailoring extraction and cleanup to specific commodity-pesticide combinations.
• Automated ASE and in-line cleanup enhance reproducibility and reduce manual handling.

Future trends and potential applications

Analytical chemistry will continue integrating high-resolution mass spectrometry, automated sample prep (robotics, in-cell cleanup), and advanced sorbents to expand analyte coverage and simplify workflows. Development of universal extraction protocols, green solvents, and real-time screening methods will further improve monitoring capabilities. Machine learning and data processing will optimize method selection and enhance identification in complex matrices.

Conclusion

No single method fully addresses the diversity of pesticide residue challenges. A combination of cryogenic or room-temperature sample processing, targeted multi-residue (QuEChERS, ASE) and single-residue approaches, along with tailored cleanup strategies, is essential. Careful validation, consideration of sample-specific issues, and method optimization remain crucial for reliable, cost-effective, and compliant pesticide residue analysis.

Reference

• 1. The Pesticide Manual, 16th Edition; British Crop Production Council, 2012.
• 2. European Commission SANTE/11945/2015. Guidance on analytical quality control and method validation.
• 3. Lehotay SJ, Cook JM. Sampling and sample processing in pesticide residue analysis. J Agric Food Chem. 2015;63(18):4395–4404.
• 10. Anastassiades M, Lehotay SJ, Štajnbaher D, Schenck F. Fast and easy multiresidue method for pesticide residues in produce. J AOAC Int. 2003;86(2):412–431.
• 19. Lehotay SJ et al. Comparison of QuEChERS sample preparation methods for pesticide residues. J Chromatogr A. 2010;1217(16):2548–2560.
• 25. Mol HGJ, de Kok A. Modification of ethyl acetate-based multiresidue method. Anal Bioanal Chem. 2007;389:1715–1754.
• 36. EURL-SRM. QuPPe-PO Method Version 9 for LC-amenable polar pesticides, 2016.
• 39. Steffens T et al. Analysis of fumigants in cereals using GC-MS/MS. Poster, EPRW 2014.
• 50. Thermo Fisher Scientific. Rocket Evaporator technical brochure, 2012.
• 53. Sun H et al. Application of accelerated solvent extraction in food analysis. J Chromatogr A. 2012;1237:1–23.