Empowering routine pesticide residue analysis in food with a GC-MS/MS platform using hydrogen as the carrier gas

Significance of the topic

Routine, high-throughput monitoring of pesticide residues in food is essential for consumer safety and regulatory compliance. Modern GC-MS/MS platforms that combine sensitive ionization, selective MS/MS detection and efficient chromatography enable laboratories to quantify hundreds of target pesticides at low parts-per-billion levels. Transitioning from helium to hydrogen as carrier gas addresses helium supply and cost challenges while preserving or improving chromatographic performance, throughput and sustainability.

Study goals and overview

This application brief evaluates a turnkey GC-MS/MS workflow for targeted quantitation of approximately 400 pesticides in food matrices using the Thermo Scientific TSQ 9610 triple quadrupole mass spectrometer equipped with an Advanced Electron Ionization (AEI) source and hydrogen carrier gas. The aim was to demonstrate limits of quantification (LOQs), linearity, accuracy, precision and robustness under routine operating conditions and to show regulatory readiness (EU SANTE guidance).

Analytical approach and methodology

• Extraction: Standard QuEChERS AOAC 2007.01 protocols for fruits and vegetables, with cleanup and solvent exchange to heptane; analytical protectant (PEG 300) and internal standards included in calibration solutions.
• Chromatography: Thermo Scientific TRACE 1610 GC with TraceGOLD TG-5MS column (20 m × 0.18 mm × 0.18 µm). Fast separations; typical GC run time 20 minutes.
• Mass spectrometry: Thermo Scientific TSQ 9610 triple quadrupole with AEI ion source operated in selected reaction monitoring (SRM) mode using hydrogen as carrier gas.
• Calibration and quantitation: Single pesticide mixture used to build a common calibration curve (range 1–100 ppb; lower limits varied per compound at 1, 2, 5 or 10 ppb). Linearity and quantifier/qualifier SRM transitions used for confirmation.
• Qualification: Linearity, LOQ determination by 10 replicate injections, repeatability (n=10) and robustness tested with QC injections interspersed among matrix extracts (apples, tomatoes, carrots) over extended injection sequences.

Used Instrumentation

• TRACE 1610 GC (Thermo Scientific)
• TSQ 9610-AEI triple quadrupole mass spectrometer (Thermo Scientific)
• TraceGOLD TG-5MS capillary column, 20 m × 0.18 mm × 0.18 µm
• TriPlus RSH SMART autosampler
• Hydrogen sensor (TRACE 1600 Series)
• LinerGOLD splitless precision liners and Instant Connect Thermospray SSL injector module

Main results and discussion

• Coverage and throughput: Method monitors ~374–400 pesticides in a single SRM method, enabling analysis with ~20-minute runs and high sample throughput.
• Linearity: Calibration curves (1–100 ppb) met validation criteria with R2 > 0.990. Relative amount deviations were <40% at the LOQ and <20% at higher levels for evaluated compounds.
• Limits of quantification: LOQs in solvent were as low as 1 ppb for many compounds; representative LOQs used in the study included 1, 2, 5 and 10 ppb depending on analyte volatility and stability. Matrix LOQs (mg/kg) were reported equivalently (e.g., 0.001–0.010 mg/kg).
• Repeatability and signal stability: Ten-replicate RSDs at LOQ for selected pesticides ranged from 6% to 19%, demonstrating acceptable repeatability at regulatory LOQs.
• Robustness: QC injections at LOQ interleaved every 10 matrix samples (apples, tomatoes, carrots) over 40 consecutive injections showed quantitation deviations within acceptance criteria without instrument tuning or maintenance, indicating robustness to matrix loading.
• AEI + hydrogen benefit: AEI improved ionization efficiency and peak shape when using hydrogen carrier gas, contributing to increased sensitivity and sharper chromatographic peaks compared with typical setups.

Benefits and practical applications

• Regulatory readiness: The workflow aligns with EU SANTE guidance for pesticide residue analysis and supports confident quantitation and confirmation through specific SRM transitions.
• Sustainability and cost: Hydrogen provides a secure, lower-cost alternative to helium while maintaining or improving chromatographic performance and run times.
• Routine lab suitability: Single-mixture calibration for ~400 analytes, minimal maintenance during prolonged sequences, and integrated software (Chromeleon CDS methods and reporting) simplify implementation in routine and regulatory laboratories.
• Complementary workflows: GC-MS/MS with this setup complements LC-MS/MS and LC-HRMS techniques to extend coverage across volatile/semi-volatile pesticides not amenable to LC-based methods.

Future trends and potential uses

• Broader adoption of hydrogen as carrier gas in routine GC-MS/MS labs to mitigate helium shortages and lower operating costs.
• Further optimization of ion sources (AEI developments) and SRM libraries to extend sensitivity to additional challenging pesticides (thermally labile or high-boiling compounds).
• Integration with high-throughput sample preparation automation, expanded multi-residue panels, and hybrid workflows combining GC-MS/MS and LC-HRMS for near-complete pesticide coverage.
• Improved software automation for data review, automated compliance checks against MRLs, and simplified method transfer between labs and regulatory schemes.

Conclusion

The TSQ 9610-AEI GC-MS/MS workflow using hydrogen as carrier gas provides a validated, robust and high-throughput solution for targeted pesticide residue analysis in food. The method demonstrated low-ppb LOQs, strong linearity, acceptable repeatability and resilience to matrix effects over extended sequences. Hydrogen adoption together with AEI enables sustainable operation without sacrificing sensitivity or regulatory compliance, making this approach well suited for routine monitoring laboratories.

References

1. European Commission. Directorate General for Health and Food Safety. Guidance document on analytical quality control and method validation procedures for pesticide residues and analysis in food and feed. SANTE/11312/2021. Implemented January 1, 2022.
2. Thermo Fisher Scientific. Application brief 004440: Empowering routine pesticide residue analysis in food with a GC-MS/MS platform using hydrogen as the carrier gas.
3. Thermo Fisher Scientific. Application brief 003163: Exploring new frontiers: empowering laboratories with the choice of helium or hydrogen as carrier gas for pesticide analysis in food using a turnkey GC-MS/MS method.
4. Thermo Fisher Scientific. Application brief 002783: An advanced integrated GC-MS/MS and LC-MS/MS workflow for the comprehensive analysis of pesticide residues.
5. Thermo Fisher Scientific. Application brief 004195: Precision pesticide analysis in food products using the TSQ Altis Plus EFOX Edition mass spectrometer — screening of over 600 regulated pesticides.
6. Thermo Fisher Scientific. Application brief 004196: Precision pesticide residue LC–Orbitrap Exploris EFOX mass detector.
7. Thermo Fisher Scientific. Application brief 004441: Routine-ready GC-MS/MS pesticide residue analysis in food.