What is automated sample preparation?

Automated sample preparation is the use of instruments and software to perform the extraction, purification, and concentration of laboratory samples with minimal human intervention. Instead of a technician manually handling solvents, cartridges, and pipettes through each step, an automated system executes the entire workflow according to a programmed method. This approach is standard practice in environmental, food safety, and contaminant testing laboratories. The sections below cover how these systems work, what they can handle, and how to select the right one for your needs.

How does automated sample preparation work?

Automated sample preparation works by replacing manual laboratory steps with a programmable instrument that controls fluid handling, extraction, and purification in a defined sequence. The operator loads samples and reagents, sets the method parameters, and the system executes each step automatically, from solvent addition and mixing through to final concentration, without requiring hands-on attention at each stage.

Most automated sample preparation systems follow the same core sequence that a manual method would use, but execute it with far greater consistency. A typical workflow includes extraction, where target compounds are drawn from the sample matrix into a solvent; cleanup or purification, where interfering compounds such as lipids, pigments, or matrix components are removed; and concentration, where the extract volume is reduced to a level suitable for instrumental analysis.

The automation layer controls critical variables that are difficult to replicate manually, including flow rates, contact times, temperature, and pressure. Because the method runs identically every time, results are highly reproducible across different operators, shifts, and days. In systems such as the GO-EHT platform, samples do not come into direct contact with the instrument itself, which eliminates the risk of cross-contamination between runs.

What types of samples can be processed automatically?

Automated sample preparation systems can process a wide range of sample matrices, including solid, semi-solid, and liquid materials. Common matrices in environmental and food safety laboratories include food and feed products, soil, sewage sludge, water, and air. The specific system configuration determines which matrices are compatible and what extraction or cleanup method is applied.

Liquid samples such as water are well suited to automated solid phase extraction platforms. Large-volume water samples, for example, can be processed through systems that handle parallel or series extraction using disk or cartridge formats, with automatic online filtration and water removal built into the workflow.

Solid and semi-solid samples such as soil, feed, fatty food products, and sludge typically require an extraction step before cleanup can begin. Solvent-based extraction systems handle this by immersing the sample in boiling solvent and recovering the extract, after which the concentrated extract passes into an automated cleanup module. This integrated approach means a single laboratory can move from raw solid sample to purified extract ready for injection with a largely unattended workflow.

What’s the difference between automated and manual sample preparation?

The key difference between automated and manual sample preparation is consistency and throughput. Manual preparation relies on a technician executing each step by hand, which introduces variability between operators and limits how many samples can realistically be processed in parallel. Automated sample preparation removes operator-dependent variability and allows multiple samples to be processed simultaneously according to a fixed, validated method.

Beyond reproducibility, the practical differences affect several dimensions of laboratory performance:

Solvent exposure: Manual methods often require open handling of organic solvents, increasing exposure risk for laboratory staff. Automated systems enclose the process and can dramatically reduce the volume of solvent used per sample.
Throughput: A single automated system can run sequences of samples consecutively or in parallel, achieving in a working day what would take multiple technicians working manually.
Operator time: Automation frees skilled analysts from repetitive pipetting and solvent handling, allowing them to focus on data review, method development, and quality control.
Traceability: Automated systems log method parameters and run data electronically, supporting audit trails required under accreditation standards such as ISO 17025.
Cross-contamination risk: Manual handling between samples creates opportunities for carryover. Systems where samples never contact the instrument hardware eliminate this risk by design.

For high-volume laboratories or those working under strict regulatory frameworks, the shift from manual to automated sample preparation is not simply a convenience, it is a quality and compliance decision.

How much solvent does automated sample preparation use?

Modern automated sample preparation systems are designed to use significantly less solvent than traditional manual methods. Many current platforms operate with fewer than 100 ml of organic solvent per sample, and advanced systems achieve this without requiring dichloromethane, a solvent that poses serious health and environmental hazards.

Traditional manual extraction methods such as Soxhlet extraction can consume several hundred milliliters of solvent per sample, and liquid-liquid extraction often requires similar volumes. When multiplied across dozens of samples per day, the cumulative solvent burden is substantial in terms of cost, waste disposal, and staff exposure.

Automated systems reduce solvent consumption through tighter process control. Flow rates are precisely managed, solvent contact times are optimized, and recovery tanks allow solvent to be collected and reused where the method permits. This reduction in solvent use is not just an environmental benefit; it also lowers reagent costs, reduces hazardous waste disposal fees, and decreases the ventilation demands placed on laboratory infrastructure.

The move toward greener laboratory practices is a genuine trend in analytical chemistry, and sample preparation automation is one of the most practical ways a laboratory can reduce its environmental footprint without compromising analytical performance.

What contaminants is automated sample preparation used for?

Automated sample preparation is used primarily for the analysis of persistent organic pollutants and other trace-level contaminants that require extensive cleanup before instrumental measurement. The most common target analytes include dioxins and furans (PCDD/Fs), polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), per- and polyfluoroalkyl substances (PFAS), polycyclic aromatic hydrocarbons (PAHs), pesticides, and polychlorinated naphthalenes (PCNs).

These compound classes share a common challenge: they are present in samples at very low concentrations, often in the parts per trillion range, while the sample matrix contains large quantities of interfering substances such as fats, pigments, sulfur compounds, and other co-extractants. Rigorous cleanup is essential before the extract can be introduced into a mass spectrometer, and that cleanup process is where automation delivers the greatest benefit.

Beyond persistent organic pollutants, automated platforms are also used for hormones and endocrine disruptors, SVOCs, mycotoxins, and emerging contaminants that are increasingly subject to regulatory monitoring. As environmental legislation expands the list of substances that must be routinely measured in food, water, soil, and air, the demand for scalable, validated automated preparation methods continues to grow.

How do you choose the right automated sample preparation system?

Choosing the right automated sample preparation system depends on four primary factors: the target analytes you need to measure, the sample matrices you routinely process, the throughput your laboratory requires, and the regulatory methods you must comply with. No single platform suits every application, so matching system capabilities to your specific analytical workload is essential.

Start by defining your analytical scope clearly:

Target compounds: Systems optimized for dioxin and PCB analysis use multilayer column cleanup chemistry that differs from PFAS-specific platforms, which require inert flow paths free of materials that can leach or adsorb fluorinated compounds.
Sample matrix: Solid samples need an extraction step before cleanup; water samples need high-volume SPE capability. Some systems handle both, while others are specialized for one matrix type.
Throughput requirements: Consider how many samples your laboratory processes per day or week, and whether you need parallel processing, consecutive batch runs, or both.
Regulatory compliance: Confirm that the system can be configured and validated against the specific EPA, CEN, or ISO methods your laboratory is accredited to perform.
Solvent and safety constraints: If your laboratory is moving away from chlorinated solvents or has strict ventilation limitations, prioritize systems that operate without dichloromethane and with enclosed solvent handling.
Integration with downstream instruments: The prepared extract must be compatible with your GC-MS/MS or LC-MS/MS system in terms of volume, solvent, and concentration. Verify that the preparation system’s output format matches your analytical instrument’s requirements.

It is also worth evaluating the supplier’s application support. A system that arrives pre-configured and tested against your target methods, with documented validation data and ongoing technical support, reduces the time from installation to accredited use considerably.

How DSP-Systems helps with automated sample preparation

DSP-Systems supplies and distributes automated sample preparation systems specifically designed for laboratories analyzing environmental contaminants and persistent organic pollutants. Their portfolio covers the full preparation workflow, from extraction through cleanup to concentration, with solutions suited to a broad range of matrices and analytes:

GO-EHT systems for fully automated purification of dioxins, PCBs, PBDEs, and PCNs across food, feed, soil, water, and air matrices, using less than 100 ml of solvent per sample and eliminating cross-contamination by design
SPE2000 for high-throughput solid phase extraction of PFAS, pesticides, PAHs, hormones, and SVOCs, processing up to 80 samples per run
AutoEmpore for large-volume water sample extraction in multi-channel configurations with automatic filtration and water removal
SER-158 for solvent extraction of solid and semi-solid samples, fully compatible with GO-EHT cleanup systems
Concentration systems including the CentriVap, MultiVap 64, and MVP Vacuum Concentrators for reliable, high-throughput evaporation and final volume adjustment

DSP-Systems also provides pre-installation programming, SPE application testing, and system configuration aligned with EPA and CEN standards, so laboratories can move from delivery to validated, accredited use as efficiently as possible. To discuss which sample preparation systems fit your laboratory’s analytical scope and throughput needs, contact the DSP-Systems team directly.

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