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Choose the right automated sample preparation platform
Selecting the right automated sample preparation platform depends on more than throughput alone. Your testing workflow, sample type, preferred sample preparation chemistry, laboratory capacity, and future scalability all influence which solution is the best fit.
Whether you're looking for a simple cartridge-based workflow or a scalable magnetic bead automation platform, Thermo Fisher Scientific offers automated sample preparation solutions designed to help improve consistency, reduce hands-on time, and support reliable downstream molecular analysis.
Start by identifying your workflow requirements, then compare the automation platforms to determine which solution best aligns with your laboratory's current and future needs.
Compare AutoMate Express and KingFisher Systems
Both Applied Biosystems AutoMate Express and KingFisher Systems automate nucleic acid extraction and purification using PrepSEQ sample preparation chemistry, but each platform is designed to address different laboratory workflows and automation requirements.
Selection factor |
AutoMate Express Systems |
KingFisher System |
Workflow format |
Closed, cartridge-based automation |
Plate-based magnetic bead automation |
Primary chemistry fit |
PrepSEQ Express cartridges |
PrepSEQ and resDNASEQ workflows |
Throughput fit |
Defined lower-batch workflows |
Medium- to high-throughput workflows |
Strong workflow association |
Mycoplasma, MMV, and vesivirus sample preparation |
Residual DNA and scalable PrepSEQ workflows |
Customer need |
I want a simplified, ready-to-run cartridge workflow. |
I want scalable plate-based automation. |
Best next step |
Why automate sample preparation?
Automating sample preparation can help laboratories improve workflow consistency while reducing the time and effort associated with manual extraction methods.
Benefits of automation include:
- Reduced hands-on sample preparation time
- Improved workflow reproducibility
- Standardized extraction protocols across operators
- Increased laboratory productivity
- Flexible throughput options to support changing testing demands
- Reliable preparation of nucleic acids for downstream qPCR analysis
Whether processing a few samples per day or supporting larger routine testing operations, automation can help laboratories streamline workflows while maintaining confidence in sample preparation performance
Choose by workflow format
The way your laboratory prepares samples is often one of the most important considerations when selecting an automation platform.
Choose the AutoMate Express System if you want:
- A closed extraction system
- Prefilled PrepSEQ Express cartridges
- Ready-to-run protocols
- Minimal setup
- A compact benchtop workflow
The AutoMate Express System is particularly well suited for laboratories looking for a standardized workflow with minimal operator interaction. The cartridge-based design simplifies setup while helping support consistent extraction performance across routine contaminant testing applications.
Choose KingFisher Systems if you want:
- Plate-based magnetic bead processing
- Flexible 24- or 96-well workflows
- Scalable automation for larger sample batches
- Automation for PrepSEQ residual DNA or related workflows
- A platform that can support broader magnetic bead-based sample preparation needs
KingFisher systems provide magnetic bead-based automation for laboratories that process larger numbers of samples or require greater workflow flexibility. The platform supports scalable sample preparation while maintaining consistent nucleic acid recovery across a variety of bioprocessing applications.
Choose by throughput
Throughput is an important consideration, but it should be evaluated alongside workflow complexity, laboratory staffing, and long-term growth plans.
Low-throughput
Laboratories processing smaller routine batches may benefit from the simplicity and efficiency of AutoMate Express systems. Its cartridge-based workflow minimizes setup while providing a straightforward approach to automated nucleic acid extraction.
High-throughput
For laboratories managing larger sample volumes or planning to expand testing capacity, KingFisher systems provide greater flexibility through plate-based automation and higher-throughput processing.
Rather than selecting a platform based solely on today's sample volume, consider how your workflow may evolve as testing demands increase.
Choose by PrepSEQ chemistry
The PrepSEQ chemistry selected for your workflow may also influence which automation platform is the best fit.
PrepSEQ chemistry |
Automation guidance |
PrepSEQ Express |
AutoMate Express systems |
PrepSEQ Residual DNA Sample Preparation Kit |
KingFisher systems, AutoMate Express systems |
PrepSEQ Nucleic Acid Sample Preparation Kit |
KingFisher systems, AutoMate Express systems |
PrepSEQ 1-2-3 Nucleic Acid Extraction Kit |
Platform depends on the validated workflow and protocol |
If you are still evaluating which PrepSEQ chemistry best supports your application, explore the PrepSEQ Sample Preparation Kits page to compare kits by workflow, sample type, and automation compatibility.
Questions to consider before selecting a platform
Before choosing an automation platform, consider the following:
- What contaminant or impurity are you testing for?
- Which PrepSEQ chemistry supports your workflow?
- How many samples do you process during a typical run?
- Do you anticipate increasing testing volumes in the future?
- Do you prefer a standardized cartridge-based workflow or a flexible magnetic bead platform?
- Will multiple users operate the instrument?
- What downstream molecular assays will you perform after sample preparation?
Answering these questions can help identify the platform that best aligns with your laboratory's current workflow while supporting future growth.
Still not sure?
If you're beginning with a specific testing application, explore the solutions we offer to identify the recommended workflow and PrepSEQ chemistry. If you've already selected your chemistry, learn more about AutoMate Express or KingFisher systems to determine which automation platform best meets your laboratory's needs.
Analytics Knowledge Hub
Explore the Analytics Knowledge Hub and discover a robust collection of webinars, articles, eBooks, infographics, and other digital resources to help you optimize analytical testing in your bioprocess workflow.
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