Finding answers before you even know the questions

Pesticide residues testing has to ensure compliance, with regard to maximum residues levels (MRLs) or tolerance levels of pesticides in foods. Analytical laboratories are expected to detect, quantitate and identify hundreds of different pesticides with diverse physicochemical properties in hundreds of different sample types, and this can be challenging.

Global pesticide regulations are constantly being updated. The most widely recognized legislation comes from the United States, Europe, Japan and China, though there are also policies set by other individual countries.

Start-to-finish workflow solutions—from the initial sample preparation techniques of QuEChERS and solid phase extraction methods, through to the analysis of hundreds of pesticides and their metabolites, targeted and non-targeted by GC-MS/MS or LC-MS/MS—demonstrate how Thermo Fisher Scientific solutions ensure reliable and efficient pesticide residue testing results while still complying with the regulatory requirements.

Laboratory Information Management Systems (LIMS)

LIMS provides full traceability of sample data for auditing compliance in a regulated environment helping food producers rapidly identify and withdraw any potentially contaminated foods. LIMS is used to improve efficiencies, productivity and sample integrity. Click the link below to read the poster on how LIMS can be used in the food safety environment.

  Read the Use of LIMS in Food Safety Testing poster

Sample preparation techniques

Sample preparation, is a generally used term that is used to transform an original sample into an analytical sample in order for it to be tested. There are several stages involved in order to get from the original sample to the analytical sample. This is especially significant when analysing analysing small quantities of samples in small-scale extraction methods.

Initial sample collection, transportation and storage to avoid cross contamination and potential degradation of residues must be considered. Sample preparation itself is the removal of the parts that should not be included in the analysis, such as soil, stones and bone fragments from the original sample of interest.

Next is a procedure known as sample processing or comminution. This can involve a number of procedures such as cutting, grinding, milling, macerating or mixing, to ensure that the analytical sample is acceptably homogeneous prior to removal of the analytical portion. Once the sample has been prepared the analytes then have to be extracted.

Extraction is the removal of analytes from the sample into the extracting phase, which is usually a solvent. In the case of pesticides residue analysis the most common extraction techniques are   QuEChERS (Quick, Easy, Cheap, Effective, Rugged and Safe) and Automated Solvent Extraction (ASE).

Finally, clean-up, which is also incorporated into the QuEChERS technique, is used to remove non-specific matrix co-extractives from the sample.

QuEChERS methods

QuEChERS (Quick, Easy, Cheap, Effective, Rugged and Safe) dispersive solid phase extraction (SPE) methods is one of the most common techniques used in modern laboratories offering a convenient and effective approach for extraction and clean-up for multi residue analysis of pesticides and herbicides in food samples such as fruit and vegetables, and other complex matrices such as meat and fish.

The QuEChERS method is a two-step process: extraction followed by clean-up.

There are four variations of the QuEChERS method currently in use:

  1. The original QuEChERS method for non-base sensitive compounds, uses sodium chloride to enhance extraction.
  2. Dispersive techniques, such as the AOAC 2007.01 method, Pesticide Residues in Foods by Acetonitrile Extraction and Partitioning with Magnesium Sulfate, uses sodium acetate as a buffer, replacing sodium chloride. This method is used for base sensitive compounds.
  3. The European Method, EN15662, is similar to the AOAC method, except the extraction uses sodium chloride, sodium citrate dihydrate and disodium citrate sesquihydrate instead of sodium acetate, as demonstrated in the Pesticide Explorer Collection.

Extraction uses salts and organic solvents to separate the analytes of interest from the food matrix. The Thermo Scientific HyperSep Dispersive SPE extraction products use magnesium sulfate (MgSO4), to aid extraction, along with either sodium chloride, sodium citrate, or anhydrous sodium acetate for base-sensitive compounds, such as folpet or captan. Available in a range of pre-prepared sorbent combinations, each kit contains the required sorbents for optimum extraction of analytes using QuEChERS methods. The organic layer is then subject to clean-up to remove any other interferences such as lipids and organic acids.

HyperSep Dispersive SPE Clean-Up products contain PSA (primary and secondary amine) for the removal of organic acids and polar pigments among other compounds. Some products couple the PSA with endcapped C18 for the removal of most lipids and sterols, or GCB (graphitized carbon black) for the removal of sterols and pigments such as chlorophyll. These are available in a range of pre-prepared sorbent combinations, each containing the necessary sorbents for optimum clean-up of analytes extracted using QuEChERS methods. Once the extracted sample is ‘clean’ it is analysed by gas or liquid chromatography / mass spectrometry.

The Table below demonstrates clean-up sorbent selection depending on matrix type:

Matrix Type Examples Sorbent Requirements for Clean-Up
General Matrices
  • Apples
  • Cucumbers
  • Melon
Removal of excess water
organic acids, fatty acids, sugar
Fatty Matrices
  • Milk
  • Cereals
  • Fish
MgSO4, PSA, C18
Additional removal of lipids and sterols
Pigmented Matrices
  • Lettuce
  • Carrot
  • Wine
MgSO4, PSA, C18, GCB
Additional removal of pigments and sterols
High Pigmented Matrices
  • Spinach
  • Red Peppers
MgSO4, PSA, C18, GCB, Chlorofiltr™
Additional removal of chlorophyll

For troubleshooting QuEChERS methods:

Problem Causes Recommended Solutions
Loss of planar pesticides Presence of GCB may result in a loss of planar compounds
  • Use a product with less GCB
  • Use the Dual Phase QuEChERS product
Loss of acidic compounds e.g. 2,4-D from starting matrix Presense of PSA will extract acidic compounds from matrix
  • Use a product containing magnesium sulfate and C18
Loss of compounds during subsequent analysis Some compounds are unstable and can break down during analysis
  • Use an analyte protectant e.g. toluene or sorbitol
Addition of sample to QuEChERS extraction tube containing sorbet causes an exothermic reaction Exothermic reaction between water in sample and magnesium sulfate
  • Add the sample to the tube, then the solvents, then the sorbent materials
Poor recovery of pesticide compounds Sample not in appropriate homogenization state
  • Wrong products used in method
  • Ensure sample is hydrated to 80% or higher
  • Verify nature of pesticides e.g. are base sensitive compounds present

Automated sample extraction

Automated sample extraction techniques include accelerated solvent extraction, automated solid phase extraction and   automated evaporation.

Accelerated Solvent Extraction (ASE) technique

Accelerated solvent extraction is often used when handling samples with a low water content, such as tea leaves and cereals, and high fat content, such as   oyster tissue. It can also be applied to the analysis of fruit and vegetables, by using a polymer, such as the Dionex™ ASE™ Prep MAP that allows quick and effective water removal.

The technique, ideal for high through-put labs, uses organic acids and aqueous solvents or acids and bases at high temperatures to increase the extraction efficiency of analytes, and high pressures to keep the solvents in a liquid state to extract compounds from solid and semi-solid samples quickly,  using small solvent volume ultimately saving time, solvent, and money, and generating results in a fraction of the time compared to traditional techniques such
as   Soxhlet or sonication.

The ASE technique, as described in the US EPA Method 3545a, takes 15–30 minutes and on average uses only 10-30ml of solvent, infiltrating the matrix more effectively so that certain types of incurred residues are extracted more effectively and thus more accurate results may be obtained.

In pesticide residues analysis, the recovery is typically checked by spiking pesticides onto the surface of the sample or even into the extract, as highlighted in the application note,   Accelerated Solvent Extraction of Pesticide Residues in Food Products.

Next, click on step 2, 3 and/or step 4 depending on your preferred analytical instrumentation solution for your pesticide residues application.

For further information on chromatography sample preparation click here.

Featured resources


Live demonstration of the Thermo Scientific Pesticide Analysis Solutions

Watch the live sample extraction and analysis demonstration on the innovative solutions for Pesticides Residue testing by Thermo Fisher Scientific.

White paper

This paper focuses on the first steps in the analytical workflow: everything you need to know about sample preparation and the most widely used methods of solvent extraction and clean-up.


Introduction to QuEChERS sample preparation technique

An introduction to QuEChERS sample preparation technique, predominately used for extraction of pesticides and other contaminants from food samples.

LC and LC-MS analysis

Food safety is an increasing concern that has resulted in stringent pesticide regulation globally. Food safety regulations require the screening and the quantitation of a large number of pesticides in food at maximum residue levels (MRL’s) generally set in the ppb-ppm range to minimize their possible negative effects on human health.

This has prompted the development of generic and reliable analytical multi-residue methods for the analysis of hundreds of pesticides by chromatography and mass spectrometry, as described in the EU guideline   SANTE/11945/2015.

LC-MS/MS enables highly selective and sensitive quantification and confirmation of hundreds of target pesticides in a single run. This method requires extensive compound-dependent parameter optimization and as such cannot be used to screen for untargeted pesticides.

Using high resolution accurate mass (HRAM) technology, in full scan, MS/MS  or both, it is possible to address these and other challenges faced by pesticides residue testing laboratories. A full scan approach, using HRAM, coupled to ultra-high pressure LC (UHPLC) is ideal for rapid and sensitive screening and detection of targeted and non-targeted LC amenable pesticide residues.

HPLC and UHPLC analytical columns provide solutions for challenging multi residue pesticides analysis, standard C18 reversed phase columns are the column of choice. However, when analysing for polar analytes, as is the case with LC-MS for pesticide residues, an aqueous C18 column is usually used—for example the Accucore aQ.

 Read   The determination of pesticides residues using LC-MS/MS (application note).

Click on Step 5, Data processing, to discover how to analyze your data.

Featured resources


The Pesticide Explorer Collection provides start-to-finish LC-MS/MS workflows for pesticide analysis, from sample prep to data analysis, tailored to help food laboratories reduce startup time and cost.

On-demand webinar

This webinar will provide pesticides residue analysts with new information from an independent thorough evaluation of the capabilities of LC–HRAM technology for the analysis of pesticide residues in QuEChERS extracts of food, including validation of quantitative and qualitative methods in compliance with international criteria.

On-demand webinar

Address critical challenges in targeted or untargeted quantitation of pesticides in food laboratories. This presentation describes the development and implementation of compete workflow solutions based on LC-MS/MS and LC-HRAM-MS/MS.

IC and IC-MS analysis

Ion chromatography (IC) offers targeted analysis and excels in analyzing ionic and polar pesticides, such as glyphosate, glufosinate and chlorate, which are not amenable to common multi-residue gas and liquid chromatography methods.

Developments in technology have enabled the use of IC-MS/MS for pesticide analysis, specifically highly polar pesticides, thermally unstable compounds and low volatility compounds, that are unable to be resolved by GC-MS techniques.

Analytes of interest are typically extracted using the   QuPPe (Quick Polar Pesticides) method. One of the main advantages with IC-MS/MS is that derivatization and multiple extraction steps before analysis are not required.

Find out more in the blog about analyzing polar pesticides including glyphosate, the world’s most widely used herbicide.

In order to obtain sufficient chromatographic retention and acceptable peak shapes, individual extracts are analyzed multiple times using different chromatographic conditions, this however does add to the overall cost of sample analysis. Overall, the use of suppressed ion chromatography coupled to an MS/MS can help to provide a more effective solution to polar pesticide residue analysis.

Click on Step 5, Data processing, to discover how to analyze your data.

Featured resources

On demand webinar

Listen to Fera Science Ltd experience, challenges and successes in the development, validation, and implementation of this approach. Learn about the critical aspects for optimization of IC-MS/MS methods for pesticides analysis.


Glyphosate is the most used pesticide throughout the world –its toxicity has been hitting the headlines recently. Glyphosate is also one of the most difficult compounds to analyze. Fortunately, it is amphoteric (can exist in different ionic forms) and that triggered a question: why not use IC?

GC and GC-MS analysis

GC-MS/MS is by far the most common approach to pesticide residue analysis. One of the main challenges with pesticide residue analysis is the ability to analyse a vast and diverse group of pesticides in a number of matrices, from simple fruits to complex matrices such as herbs, spices and tea, while at the same time having have high throughput, fast turn around and a low cost of analysis .

The benefit of using GC-MS/MS is its ability to evaluate a wide scope of multi analyte residues for pesticides offering good separations for targeted quantitative analysis.

Currently, more than 300 regulated pesticides can be analyzed by this technique. International regulations on the maximum residue levels of pesticides in food (MRLs) cover hundreds of individual  target components at very low maximum residue limits—in the range of 10 ppb or lower, achieved by GC-MS/MS. Baby food, for example is of particular importance because babies are more vulnerable to adverse health effects from these chemicals. Read the application note.

GC-MS/MS HRAM offers full scan targeted and non-targeted acquisition and provides the required sensitivity and selectivity in complex matrices for routine pesticides screening and quantification. It enables the detection and identification of unknown compounds. The use of GC coupled with HRAM offers fast, high-throughput   pesticide residues analysis in baby food samples for example, with an almost unlimited scope in the analysis through full scan acquisition. Quantitative performance is comparable to GC-MS/MS and in compliance with   SANTE/11945/2015 guidelines.

GC columns specifically designed for pesticides analysis allow the separation of compounds of interest, with high performance, sensitivity, and reproducibility.

Click on Step 5, Data processing, to discover how to analyze your data.

Featured resources

Application note

Targeted screening methods require optimization of acquisition parameters for compounds. The scope of analysis can be increased using high-resolution full-scan mass spectrometry.

Application note

Read how the latest technology is used to identify pesticides inline with current guidelines.

On-demand webinar

Learn the capabilities and potential application of GC-HRAM technology for the analysis of pesticide residues in QuEChERS extracts of food and validation of the methods in compliance with international criteria.

Data processing

Fully automated chromatography data system (CDS) software is now common place in routine pesticide analysis laboratories. This software allows instrument control, automation, data processing, and more.

CDS unifies the workflows for chromatography and routine quantitative MS analysis. It provides full integration of GC-MS/MS, LC-MS/MS, and IC-MS/MS instruments and analyses can be run from method creation to final reporting.

Read the blog: How to Find the Most Suitable Method for the Analysis of Pesticides.

Data processing for pesticide residue analysis allows for streamlined targeted screening and quantitation for all compound types. An example of data processing software for quantitative and qualitative purposes in pesticide residues testing is shown in   the application note.

Easy access to all necessary information for hundreds of compounds in seconds and allows the transformation of any data from anywhere into a method. It also can be tailored for food safety applications and provides the ability to meet worldwide regulations.

Compound Discoverer Software allows for data analysis for small molecule identification. Researchers are able to strategically collect, organize, store and report data for both targeted and untargeted high resolution analyses.

Featured resources


Introduction to Chromeleon CDS

Run instruments using the same intuitive user interface, with the same methods, and provide results in the same format. Operate any instrument, any time.


Compound databases for SRM and HRAM workflows and the software’s Method Forge™ ensures easy access to hundreds of molecules in seconds. Download a free trial of the new TraceFinder 4.0 software today.


The only small molecule analysis solution able to make full use of the high-resolution accurate-mass (HRAM) data.

Attend the virtual conference from your desk. View the talks as if you were present and download the presentations for future reference plus listen to short interviews from participants at the event.

A consolidation of our expertise and technologies into a resource to guide through even the most challenging of your pesticides analyses.

Search all pesticide residues testing resources

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Resource Number
Application Brief Extraction of Organochlorine Pesticides from Oyster Tissue Using Accelerated Solvent Extraction Sample Preparation AB152
Application Note Fast Screening, Identification, and Quantification of Pesticide Residues in Baby Food Using GC Orbitrap MS Technology GC and GC-MS AN10449
Application Note Three-fold Increase in Productivity for Pesticide Residue Analysis in Baby Food Using Fast Triple Quadrupole GC-MS/MS GC and GC-MS AN10432
Application Note Trace Determination of Organo-Phosphorous Pesticides in Olive Oil by GC Analysis GC and GC-MS AN10049
Application Note Analysis of Dithiocarbamate Pesticides by GC-MS GC and GC-MS AN10333
Application Note Multi-Residue Pesticides Analysis in Herbal Tea Products by GC-MS/MS GC and GC-MS  
Application Note Rapid Analysis of Pesticides in Difficult Matrices Using GC/MS/MS GC and GC-MS AN51880
Application Note Rapid analysis of 303 Pesticide Residues in Green Bean Using Triple Quadrupole GC-MS/MS GC and GC-MS AN52022
Application Note High Sensitive MID Detection Method for Toxaphenes by High Resolution GC/MS GC and GC-MS AN30128
Application Note Fast Multi-residue Pesticide Analysis using Triple Quad GC-MS/MS GC and GC-MS AN10263
Application Note Fast GC-MS/MS for High Throughput Pesticides Analysis GC and GC-MS AN52027
Application Note Multi-residue pesticide screening in cereals using GC-Orbitrap mass spectrometry GC and GC-MS AN10541
Application Note Pesticide residues screening analysis in tea and honey using a Q Exactive Focus High Resolution Mass Spectrometer GC and GC-MS AN64938
Application Note Routine analysis of polar pesticides in water at low ng/L levels by ion chromatography coupled to triple quadrupole mass spectrometer IC and IC-MS AN64945
Application Note Analysis of Triazines Using a Thermo Scientific Accucore XL C8 4 µm HPLC Column LC and LC-MS AN20541
Application Note UHPLC Separation of Triazine Herbicides at Elevated Temperature LC and LC-MS AN453
Application Note Separation of Eighteen Pesticides using Accucore RP-MS HPLC Column LC and LC-MS ANCCSCETHERBS
Application Note Separation of Urea Herbicides using a Core Enhanced Technology Accucore HPLC Column LC and LC-MS ANCCSCETHERB
Application Note Analysis of Triazine Pesticides using a Core Enhanced Technology Accucore HPLC Column LC and LC-MS ANCCSCETPEST
Application Note Quantitative and Qualitative Confirmation of Pesticides in Beet Extract Using a Hybrid Quadrupole-Orbitrap Mass Spectrometer LC and LC-MS AN617
Application Note Fast and Ultrafast LC-MS/MS Methods for Robust and Reliable Analysis of Pesticides in Food Using the Vanquish UHPLC System LC and LC-MS AN1138
Application Note Fast Routine Analysis of Polar Pesticides in Foods by Suppressed Ion Chromatography and Mass Spectrometry IC and IC-MS AN64868
Application Note Robust LC-MS Analysis of Pesticides with 1.0mm i.d. Column Using the Vanquish Horizon UHPLC System LC and LC-MS AN72162
Application Note Increasing Translational Proteomics Workflow Efficiency: Ultra-High Performance Liquid Chromatography with pSMART Data Acquisition and Processing LC and LC-MS AN64581
Application Notebook Food Safety Applications Notebook: Agricultural Chemical Contaminants Sample Preparation AN-LPN3036
Application Notebook Accelerated Solvent Extraction Environmental Applications Summary Notebook: Pesticides, Chlorinated Compounds, POPs Sample Preparation AI70318
Application Notebook GC and GC-MS Applications Notebook for Food Safety Analysis  GC and GC-MS AI10382
Application Notebook Food Safety Applications Notebook: Agricultural Chemical Contaminants LC and LC-MS ANLPN3036
Article Extraction and Measurement of GC-Amenable Pesticides in Difficult Matrices GC-MS -
Article Orbitrap GC-MS for Quantitative and Qualitative Multi-residue Analysis of Pesticides GC-MS -
Article Pesticide Residues in Fruits and Vegetables LC-MS -
Article Multi-residue analysis of pesticides by GC-HRMS GC-MS -
Article The Role of Ion Chromatography in Food Safety Laboratories IC-MS -
Article Screening and Targeted Routine Quantitation of Pesticide Residues in Food Products LC-MS -
Article GC-Orbitrap MS Technology for Pesticides Analysis GC-MS -
Brochure Finding ANSWERS before you even know the questions. GC and GC-MS BR90159
Brochure Scoprire LE RISPOSTE ancor prima di conoscere le domande GC and GC-MS BR90159
Brochure Encontrar RESPUESTAS antes de incluso saber las preguntas GC and GC-MS BR90159
Brochure Trouver LES RÉPONSES avant même que vous ne vous posiez les questions GC and GC-MS BR90159
Brochure Wir beantworten FRAGEN, die Sie noch gar nicht kennen GC and GC-MS BR90159
eBook Advancing the Analysis of Pesticides and Other Chemical Residues Workflow  
Infographic Pesticide Residue Testing Infographic – The Future Starts Here GC and GC-MS XX72032
Poster Note Broad Scope Pesticide Screening in Food Using Triple Quadrupole GC-MS GC and GC-MS ASMS13
Poster Note Analysis of Pesticide Residue in Green Tea Extracted by QuEChERS with Acetonitrile as Final Solvent GC and GC-MS PN10391
Technical Guide Determination of Pesticides in Grapes, Baby Food and Wheat Flour by Automated Online Sample Preparation LC-MS/MS Sample Preparation TG52213
Technical Guide Validation of the Method for Determination of Pesticide Residues by Gas Chromatography – Triple-Stage Quadrupole Mass Spectrometry GC and GC-MS TG63899
Technical Guide Determination of Carbendazim and Benomyl Residues in Oranges and Orange Juice by Automated Online Sample Preparation Using TLX-LC-MS/MS LC and LC-MS TG52292
Technical Note Analysis of Pesticide Residues in Lettuce Using a Modified QuEChERS Extraction Technique and Single Quadrupole GC/MS Sample Preparation TN10222
Technical Note Multi-residue Pesticide Analysis in Onion by a Modified QuEChERS Extraction and Ion Trap GC/MSn Analysis Sample Preparation TN10238
Technical Note Multi-residue Pesticide Analysis in Rice by a Modified QuEChERS Extraction and Ion Trap GC/MSn Analysis Sample Preparation TN10239
Technical Note Multi-residue Pesticide Analysis in Green Tea by a Modified QuEChERS Extraction and Ion Trap GC/MSn Analysis GC and GC-MS TN10295

Finding answers before you even know the questions

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