How do you integrate automated systems into an existing lab workflow?

Bringing automated systems into an established laboratory is rarely a plug-and-play exercise. Whether the goal is faster throughput for PFAS SPE automation, more reproducible PBDE analysis automation, or simply reducing the solvent burden on analysts, the transition requires deliberate planning. Done well, laboratory automation transforms both the quality and the pace of analytical work. Done poorly, it creates bottlenecks, method failures, and frustrated staff. The sections below walk through a structured approach to integration that minimises disruption and maximises the return on investment in new equipment.

Mapping your current lab workflow before automation

Before any new system arrives on the bench, it is essential to document exactly how samples move through the laboratory today. This means tracing every step from receipt and registration through extraction, cleanup, concentration, and final instrument injection. The goal is to identify where time is lost, where errors most commonly occur, and where manual steps introduce variability that affects data quality.

Pay particular attention to the cleanup and extraction stages. These are typically the most labour-intensive parts of sample preparation, and they are also where automation delivers the greatest gains. Record the solvents used, the cartridge formats, the sample volumes, and the approximate time each step demands per analyst. This baseline data will later serve as the benchmark against which automated performance is measured, making it far easier to demonstrate the value of the new system to management or accreditation bodies.

It is equally useful to map dependencies. If a concentration step relies on the extraction being completed by a certain time, or if instrument scheduling dictates when cleaned samples must be ready, those constraints need to be visible before a new system is introduced. Automation does not eliminate scheduling complexity; it shifts it, and understanding the existing rhythm of the lab prevents the new equipment from creating unexpected conflicts downstream.

Matching automated systems to your sample matrices and contaminants

Not every automated platform is suited to every analytical challenge, and selecting the wrong system for a given matrix or target compound class is one of the most common and costly integration mistakes. The choice of equipment should be driven by the specific contaminants being measured, the matrices being processed, and the regulatory methods the laboratory is required to follow.

For laboratories working with persistent organic pollutants such as dioxins, PCBs, PBDEs, and PCNs across matrices like food, feed, soil, sewage sludge, and air, fully automated purification systems designed around multi-layer column cleanup are the appropriate starting point. These platforms handle complex lipid-rich matrices and deliver the selectivity required for trace-level analysis without exposing analysts to hazardous solvents. Systems operating with less than 100 ml of solvent per sample and eliminating dichloromethane entirely represent a meaningful step forward in both safety and environmental performance.

For PFAS SPE automation and the extraction of pesticides, hormones, SVOCs, and PAHs from water or other liquid matrices, solid phase extraction platforms with multi-channel capability and support for a range of disk and cartridge formats are better suited. The ability to process samples in parallel or series mode, and to handle large volumes through online filtration, is particularly important when regulatory programmes require high sample throughput within tight turnaround windows.

Solid and semi-solid sample matrices introduce an additional extraction step before cleanup. Systems based on the Randall principle, which perform extraction directly in boiling solvent followed by a hot Soxhlet or Twisselmann step, are well established for this purpose and can be integrated as the upstream stage of a fully automated preparation workflow. Matching each stage of the workflow to the right instrument, rather than forcing a single platform to do everything, is the foundation of a well-designed automated laboratory.

Phased integration: running automated and manual methods in parallel

Switching an entire laboratory over to automated sample preparation in a single step is rarely advisable, particularly in accredited environments where method changes require formal validation and documentation. A phased approach, in which the automated system runs alongside the existing manual method for a defined period, is both safer and more informative.

The parallel running phase serves several purposes simultaneously. It allows analysts to build familiarity with the new system under real working conditions rather than in a purely training context. It generates the side-by-side data needed to demonstrate method equivalence, which is a prerequisite for updating accreditation scope under ISO 17025. It also provides an early warning of any matrix-specific issues that may not have been apparent during the initial equipment selection process.

Define clear criteria before the parallel phase begins. Specify how many samples need to be processed in parallel, what statistical agreement between methods is acceptable, and how long the phase will run. Laboratories that leave these criteria vague often find the parallel phase extending indefinitely, which delays the efficiency gains that justified the investment in the first place. A structured exit criterion keeps the project moving forward.

During this phase, it is also worth identifying which sample types are best suited to early transition and which should be held back. Routine, well-characterised matrices with stable analytical results are the ideal candidates for early automation. Complex or infrequent matrices with known interference challenges are better validated later, once the team has confidence in the system’s behaviour under standard conditions.

Staff training and method validation for new systems

Technical competence with a new automated system does not develop automatically, even among experienced analysts. Structured training that covers both instrument operation and the underlying analytical principles is essential for ensuring that staff can troubleshoot problems independently rather than relying on the equipment supplier every time an unexpected result appears.

Training should address, at minimum, the following areas:

Instrument startup, shutdown, and routine maintenance procedures
Software operation including sequence programming, method editing, and data export
Cartridge and consumable loading, including correct handling to avoid contamination
Interpretation of system logs and diagnostic outputs
Recognition of common failure modes and the steps to resolve them

Method validation for automated systems follows the same general framework as validation for manual methods, but there are additional parameters worth examining carefully. Carryover between samples is particularly important in systems where flow paths are shared, and it should be tested systematically across the concentration range expected in routine analysis. Recovery, repeatability, and reproducibility should be assessed using certified reference materials or spiked samples that reflect the matrices the laboratory processes most frequently.

Documentation is not a bureaucratic afterthought. Thorough records of the validation process, including raw data, statistical summaries, and any deviations from the planned protocol, are what allow an accreditation assessor to follow the laboratory’s reasoning. They also provide the institutional memory that protects the laboratory when staff turn over and new analysts need to understand why specific method parameters were chosen.

Common integration challenges and how to address them

Even well-planned automation projects encounter difficulties, and being aware of the most common challenges in advance makes it easier to respond effectively rather than reactively.

Solvent compatibility and system inertness. Automated SPE platforms used for PFAS analysis must have fully inert flow paths that are free of materials capable of leaching fluorinated compounds. Introducing a system with incompatible materials into a PFAS workflow does not just affect results; it can invalidate an entire analytical sequence and compromise accreditation. Verify material specifications before purchase and confirm compatibility with the solvents and analytes in use.

Integration with laboratory information management systems (LIMS). Automated systems generate structured data, but that data needs to flow into the laboratory’s broader information management environment without manual transcription. Establishing the data export format and the interface between the instrument software and the LIMS early in the project avoids a situation where automation speeds up sample processing but creates a new bottleneck in data handling.

Throughput mismatches between workflow stages. If an automated extractor can process 80 samples per run but the downstream concentration step can only handle a fraction of that volume at once, the overall throughput gain is limited by the slowest stage. Mapping the full workflow, as described in the first section, helps identify these mismatches before they become operational problems. Multi-channel parallel evaporation systems and high-capacity vacuum concentrators are often the solution when concentration is the limiting step.

Resistance to change among experienced staff. Analysts who have developed highly refined manual techniques over many years sometimes view automation with scepticism, particularly if they associate it with a loss of professional judgement. Involving senior analysts in the validation process and in decisions about method parameters goes a long way toward building ownership of the new approach rather than opposition to it.

How DSP-Systems helps with laboratory automation integration

DSP-Systems supports laboratories at every stage of the automation journey, from initial workflow assessment through equipment selection, installation, method validation, and ongoing technical support. As an automated sample preparation specialist, the company offers a curated portfolio of systems matched to the specific demands of environmental contaminant analysis:

The GO-EHT fully automated purification platform for dioxins, PCBs, PBDEs, and PCNs across food, feed, soil, water, and air matrices
The SPE2000 for high-throughput PFAS SPE automation and extraction of pesticides, hormones, SVOCs, and PAHs, processing up to 80 samples per run
The AutoEmpore for large-volume water sample extraction with multi-channel flexibility and automatic online filtration
The SER-158 for automated extraction of solid and semi-solid samples using less than 100 ml of solvent per sample
Evaporation and concentration systems including the MultiVap 64 and CentriVap for post-extraction sample handling

DSP-Systems also provides pre-installation programming, SPE application testing, and configuration aligned with EPA and CEN standards, so laboratories can move through the validation phase with confidence. To discuss how automated systems can be integrated into your specific workflow, get in touch with the DSP-Systems team directly.