Fragment Analyzer Systems

5400 Fragment Analyzer System

The 5400 Fragment Analyzer system redefines the bounds of nucleic acid QC analysis by using automated parallel capillary electrophoresis. Capable of interfacing with world leading robotic systems, analysis of DNA and RNA samples can now be performed around-the-clock through robotic integration.

The 5400 Fragment Analyzer system is compatible with all the same high-quality reagent kits available for the 5300 Fragment Analyzer system. Use quantitative kits for analyzing NGS libraries, large fragment smears, genomic DNA, RNA, and small RNA. Additionally, you can use qualitative kits for analyzing PCR amplicons, SSRs/microsatellites, CRISPR generated mutations, or digested DNA.


  • Robotic Integration - A custom API and powered drawers offer seamless integration with most laboratory automation systems
  • High Throughput Separations - Unattended analysis of more than 2,400 samples every 24 hours
  • High Separation Resolution - Resolve a wide range of DNA and RNA fragments. Achieve as low as 3 bp resolution with high sizing accuracy for fragments under 300 bp
  • Low Cost per Sample - Choose qualitative or quantitative gel kits that best suit your analysis needs. Realize lower operational costs than other analytical instruments
  • Decreased Prep Time - With room temperature stable reagents and no daily array handling, minimal work is needed to setup runs
  • Wide Dynamic Range - Most reagent kits cover approximately two orders of magnitude. High and Standard Sensitivity Kits are available for most applications, extending the overall range of detection
  • User-Friendly Software - Automate data scoring. Calculate fragment size and concentration. Create, save, and load customized reports and scoring parameters for flagging and smear analysis
  • IQ/OQ services available for use in GMP environments
  • Desktop PC supplied with a comprehensive 3-year warranty through HP


Ambient Temperature 20-23 °C
Dimensions (WxDxH) 35 cm x 61 cm x 86 cm
Line Frequency 47-63 Hz
Line Voltage 100-240 VAC
Number of Samples per Run 96
Operating Environment Relative Humidity 20-80 %
Power Consumption 150 VA
Weight 38.5 kg

How It Works

5400 Fragment Analyzer

The 5400 Fragment Analyzer system uses the same 96-capillary arrays as the 5300 Fragment Analyzer system. These robust arrays help the system separate over 2,400 samples in 24 hours without sacrificing separation resolution or quantification accuracy. 

Controlled through a detailed and rigorously tested API (Application Program Interface), the 5400 Fragment Analyzer system is fully configured for seamless and continuous operation. The API controls the movement of the buffer, waste, and sample drawers. The electrophoresis methods are activated through either TCP/Ethernet or serial port connections. Customized API commands can be coded to adapt to any work environment.

With integrated software packages for both operation and analysis, the 5400 Fragment Analyzer system allows users to remotely control electrophoresis runs and have result files generated and formatted to specific user criteria. Auto-data processing can be activated for large-scale assessment post-electrophoresis. Additionally, sample names can be added through LIMS integrated sample data files.


Automated fragment analysis with the 5400 Fragment Analyzer system

The Agilent 5400 Fragment Analyzer is a robust system for automated fragment analysis with the flexibility to integrate into a variety of laboratory robotic systems. Capable of running 96 samples in parallel, the capillary electrophoresis system performs high-throughput automated DNA and RNA fragment analysis with high resolution. Reliably assess the quality and integrity of your small or large fragments with the 5400 Fragment Analyzer system.