What types of samples can be processed with automation?

Automated sample preparation systems can process a remarkably broad range of sample types, including solid materials like soil, food, and feed, as well as liquid matrices such as water, blood, and environmental extracts. Modern laboratory automation is designed to handle diverse matrices with consistent precision, making it suitable for virtually any laboratory workflow focused on environmental contaminant analysis. The sections below explore exactly which matrices qualify, how different sample states are handled, and where the practical boundaries of automation lie.

Which sample matrices are compatible with automated preparation systems?

Automated sample preparation systems are compatible with a wide range of matrices, including food, feed, soil, sewage sludge, water, air, and biological tissues. The key requirement is that the sample can be introduced into the system in a form the instrument can process, whether as a raw solid, a liquid extract, or a pre-digested material. Compatibility is determined by the contaminant target, the extraction principle used, and the system’s design.

In practice, automated sample preparation covers the following major matrix categories:

Food and feed: Meat, fish, eggs, dairy, cereals, oils, and animal feed are among the most commonly automated matrices, particularly for dioxin, PCB, and pesticide monitoring programs.
Environmental solids: Soil, sediment, sewage sludge, and compost can all be processed, typically after an initial extraction step that converts the solid into a liquid extract ready for cleanup.
Water samples: Surface water, groundwater, wastewater, and drinking water are handled through large-volume extraction systems, particularly for PFAS, pesticides, and other emerging contaminants.
Air and particulate matter: Air filter extracts and dust samples fall within the scope of automated purification platforms designed for persistent organic pollutants.
Biological and industrial materials: Blood, tissue, and certain industrial raw materials can also be processed, depending on the system configuration and the analytical target.

The breadth of compatible matrices reflects the fact that environmental contamination does not respect category boundaries. A laboratory monitoring dioxins, for example, may need to analyze feed, soil, and water within the same workflow, and modern automated platforms are built to accommodate exactly that kind of versatility.

How does automation handle solid versus liquid samples differently?

Automation handles solid and liquid samples through fundamentally different extraction mechanisms before the cleanup stage begins. Solid samples require a physical extraction step to release contaminants into a solvent phase, while liquid samples can be loaded directly onto extraction media. Both pathways then converge at the purification and concentration stage, where automation delivers the greatest consistency gains.

Solid sample extraction

Solid matrices such as soil, food tissue, and sludge must first be converted into a liquid extract. Systems based on the Randall principle, for example, perform extraction directly in boiling solvent, followed by a hot Soxhlet or Twisselmann step to maximize recovery. The SER-158 operates on this principle, processing up to six solid or semi-solid samples in approximately 23 hours while using less than 100 mL of solvent per sample. Solvents are recovered and recirculated during the process, minimizing waste and reducing concentration time. Once extraction is complete, the resulting liquid extract moves seamlessly into automated cleanup.

Liquid sample extraction

Liquid matrices such as water samples are handled through direct loading onto solid phase extraction media. Large-volume water samples present particular challenges because the volumes involved can reach hundreds of millilitres, and automated systems must manage filtration, loading speed, and solvent elution without operator intervention. Systems designed for this purpose support multiple disk and cartridge formats, operate in parallel or series mode to match throughput requirements, and include automatic online filtration and water removal to keep the process uninterrupted.

After extraction, both solid-derived and liquid-derived samples follow the same downstream path: purification to remove matrix interferences, followed by concentration to the precise end volume required for instrumental analysis.

What contaminants can be targeted across these sample types?

Across the full range of compatible matrices, automated sample preparation systems can target a broad spectrum of environmental contaminants, including dioxins and furans (PCDD/Fs), polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), polychlorinated naphthalenes (PCNs), PFAS compounds, pesticides, polycyclic aromatic hydrocarbons (PAHs), hormones, and other semi-volatile organic compounds (SVOCs).

The contaminant target largely determines which system configuration is required. Persistent organic pollutants such as dioxins and PCBs demand highly selective multi-layer cleanup to remove co-extracted lipids and matrix interferences before mass spectrometry measurement. PFAS analysis, by contrast, requires systems with inert flow paths free of materials that could leach or adsorb fluorinated compounds. Pesticide and hormone residue analysis often involves high-throughput SPE platforms capable of processing large batches across diverse matrices in a single run.

In 2026, the expanding regulatory focus on emerging contaminants means laboratories are increasingly expected to monitor multiple compound classes within the same sample batch. Automated platforms that support flexible cartridge configurations and programmable elution sequences are well positioned to meet this demand without requiring separate manual workflows for each analyte group.

Are there sample types that automation cannot process reliably?

While automated sample preparation covers the vast majority of matrices encountered in environmental and food safety laboratories, certain sample types present genuine challenges. Highly viscous materials, samples with extreme fat content, matrices with very high particulate loads, and samples requiring complex digestion steps before extraction can exceed the practical scope of standard automated platforms without additional manual pre-treatment.

Specifically, the following situations may require manual intervention or hybrid workflows:

High-fat matrices: Samples such as pure animal fat or certain oils may require preliminary fat reduction steps before automated cleanup can proceed effectively. Without this, column overloading and poor recovery become likely.
Very heterogeneous solids: Samples that cannot be homogenized to a consistent particle size may produce variable extraction efficiency, since the extraction principle assumes reasonably uniform contact between solvent and sample material.
Samples requiring acid or alkaline digestion: Certain biological or industrial matrices need chemical digestion before extraction, a step that is typically performed manually before the automated workflow begins.
Very low-volume samples: Micro-samples or precious clinical specimens that cannot be replicated may require specialized handling beyond standard automated platforms.

It is worth noting that these limitations are narrowing as instrument design evolves. Many systems now incorporate pre-treatment modules or can be coupled with upstream preparation steps, progressively reducing the number of matrix types that fall outside the automated workflow.

How does automated processing reduce cross-contamination risk across sample types?

Automated processing reduces cross-contamination risk primarily by eliminating direct contact between the sample and the instrument’s internal surfaces. In systems where samples are processed within sealed or single-use containers and never touch shared flow paths, carryover between consecutive samples becomes structurally impossible rather than merely unlikely. This design principle is especially important in laboratories analyzing persistent organic pollutants, where trace-level contamination can invalidate results.

Several engineering approaches contribute to this protection:

No-contact processing: Systems where samples do not come into direct contact with the instrument eliminate the primary route of cross-contamination between runs.
Inert flow paths: Automated SPE systems with fully inert materials resistant to all organic solvents prevent adsorption of analytes onto system surfaces, which is particularly critical for PFAS analysis where Teflon and other fluoropolymers can act as contamination sources.
Single-use consumables: Disposable cartridges, disks, and collection vials ensure that no residue from a previous sample enters the next extraction cycle.
Controlled solvent volumes: Precise, automated solvent delivery prevents over-washing or under-washing that can cause carryover in manual procedures.

Beyond instrument design, automation also removes the variability introduced by multiple analysts handling samples at different stages. When every step from loading to elution follows an identical programmed sequence, the risk of human error, accidental contact, or inconsistent technique is eliminated as a contamination source.

Which industries rely most on automated sample preparation for these matrices?

The industries that rely most heavily on automated sample preparation are environmental monitoring, food and feed safety, water quality testing, and industrial hygiene. Each of these sectors requires high-throughput analysis of complex matrices for regulated contaminants, making manual sample preparation both a bottleneck and a quality risk.

In the food and feed industry, regulatory frameworks in the European Union and globally mandate monitoring of dioxins, PCBs, and pesticides across a wide range of commodities. Laboratories processing hundreds of samples per week cannot sustain that volume with manual cleanup methods while maintaining the precision that accreditation standards require. Automation is not a convenience in this context but a practical necessity.

Environmental testing laboratories face similar pressures. Soil, water, and air monitoring programs generate large, continuous sample streams, often under tight turnaround requirements. Automated extraction and purification allow these laboratories to maintain throughput without expanding staff or compromising data quality.

The PFAS sector has become one of the fastest-growing application areas for laboratory automation. As regulatory limits for per- and polyfluoroalkyl substances become more stringent and the number of regulated compounds expands, laboratories need platforms capable of handling large water volumes and complex matrices with the sensitivity and reproducibility that low-level PFAS detection demands.

Pharmaceutical and clinical research laboratories also use automated sample preparation for hormone analysis, toxicological screening, and pharmacokinetic studies, though the specific systems and methods differ from environmental applications. Industrial hygiene monitoring, including workplace air and surface sampling for chemical exposure assessment, rounds out the major sectors where automation delivers measurable analytical and operational benefits.

How DSP-Systems helps with automated sample preparation across sample types

DSP-Systems provides laboratories with a complete portfolio of automated sample preparation solutions covering the full range of matrices and contaminant targets described in this article. Whether your laboratory processes food, water, soil, or air samples, DSP-Systems offers purpose-built platforms to match your workflow:

GO-EHT systems for fully automated purification of dioxins, PCBs, PBDEs, and PCNs across food, feed, soil, sludge, water, and air matrices, using less than 100 mL of solvent per sample without dichloromethane
SPE2000 for high-throughput solid phase extraction of PFAS, pesticides, hormones, SVOCs, and PAHs, processing up to 80 samples per run across a wide range of cartridge formats
AutoEmpore for large-volume water sample extraction with automatic online filtration, available in multiple channel configurations for parallel or series operation
SER-158 for efficient extraction and concentration of solid and semi-solid samples, fully compatible with GO-EHT cleanup systems for an integrated end-to-end workflow
Expert support for method development, system configuration to EPA and CEN standards, and pre-installation programming tailored to your specific matrices and targets

If you want to find out which automated system best fits your laboratory’s sample types and analytical requirements, contact DSP-Systems directly for expert guidance.

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