5400 Fragment Analyzer

The 5400 Fragment Analyzer redefines the bounds of automated QC analysis of nucleic acids. Capable of interfacing with world leading robotic systems, analysis of DNA and RNA samples can now be performed around-the-clock.

AATI Scientist looking at data

The 5400 Fragment Analyzer, specially designed for high-throughput laboratories of all kinds, is built on the proven frame of the Fragment Analyzer utilizing our state of the art 96 capillary array. Coordination with the leading robotic automation developers has ensured the 5400 Fragment Analyzer effortlessly integrates into most robotic workflows. Notably, each drawer is controlled and able to interface with a robotic arm. With seamless integration into an automated workflow, the 5400 Fragment Analyzer can size, qualify, and quantify nucleic acid samples around-the-clock without human intervention, analyzing over 2,400 nucleic acid samples per day.

The 5400 Fragment Analyzer is compatible with all the same high quality reagent kits available for the Fragment Analyzer. Perform large scale analysis of genomic DNA for NGS workflows or screen for CRISPR induced mutations. No matter your application, the 5400 Fragment Analyzer is the ideal high-throughput solution for DNA analysis and RNA analysis.

What is the 5400 Fragment Analyzer?

The 5400 Fragment Analyzer is the only parallel capillary electrophoresis instrument for the QC analysis of nucleic acids capable of seamless incorporation into laboratory automation systems. Capable of analyzing thousands of DNA and RNA samples per day, the 5400 Fragment Analyzer takes nucleic acid analysis to the next level. No matter how many samples need to be analyzed, post-separation data analysis is a breeze with the proprietary ProSize Data Analysis Software and auto-data processing.

High Separation Resolution
Resolve a wide range of DNA and RNA fragments. Achieve as low as 3 bp resolution with high sizing accuracy.
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.
Robotic Integration
Capable of integrating with most laboratory automation systems.
Wide Dynamic Range
Most gel 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.

How Sensitive is the 5400 Fragment Analyzer?

Though designed for high-throughput laboratories, the 5400 Fragment Analyzer maintains a high degree of versatility. Capable of integrating with most laboratory automation systems, it can process thousands of samples per day. Furthermore, the 5400 Fragment Analyzer uses all the high-quality reagent kits developed for the Fragment Analyzer, bringing a high-throughput solution to the full spectrum of DNA and RNA analysis.

Flexible enough to handle any workflow scenarios

Designed for automated, high-throughput laboratories, the 5400 Fragment Analyzer confidently quantifies, qualifies, and sizes diverse nucleic acids for a wide range of applications, saving time and money.
A robustly designed capillary array enables the separation of over 2,400 nucleic acid samples per day without sacrificing resolution or quantification accuracy.
Automated drawers interface with most robotic arms for seamless integration into most laboratory automation systems.
Load up to two different gels and program distinct methods that require different gel matrices.

ProSize Data Analysis Software

An efficient workflow is crucial to high-throughput laboratories. Quick, quality results mean downstream applications are reached sooner and conclusions are made faster. With the option of Batch Data Processing, ProSize Data Analysis Software reduces post-electrophoresis data bottlenecks, providing you with the results you need, when you need them. Integration with a LIMS system allows for the automatic labeling of samples in the software, further streamlining your workflow.

Batch Data Processing with PROSize Data Analysis Software provides high volume data processing to high-throughput nucleic acid analysis workflows.

Batch Data Processing with PROSize Data Analysis Software provides high volume data processing to high-throughput nucleic acid analysis workflows.

The 5400 Fragment Analyzer is fully compatible with all the kits rigorously designed for use with the Fragment Analyzer. The product of dedicated research, development, and quality control, the reagent kits for the 5400 Fragment Analyzer provide accurate quantification and qualification of a wide variety of DNA and RNA sample types.


A quality metric developed by Illumina
for ProSize. Provides unmatched assessment of FFPE RNA quality prior to sequencing through analysis of formalin-fixed, paraffin-embedded (FFPE) RNA
tissue before running in TrueSeq.
Learn more
Quickly quantify and
qualify DNA and RNA samples
with ProSize Data Analysis
Software. Data is automatically processed and an electropherogram, digital gel image, and a summary of nucleic acid size and concentration
are provided. Further analysis tools
are available to meet unique
user demands.


Eliminate unnecessary sequencing
from CRISPR workflows. When used in conjunction with the CRISPR family of reagent kits from Agilent - formerly AATI,
the CRISPR Plugin identifies
positive clones,providing %Cleaved, %Mutation, and zygosity.


The 5400 Fragment Analyzer is well suited to the same applications as the Fragment Analyzer, but at a much higher throughput capacity. Able to run over 2,400 samples per day without human intervention, the 5400 Fragment Analyzer is ideal for high-throughput genotyping, CRISPR mutation screening, and NGS workflows.


CRISPR gene editing has swept the life sciences by storm. Use the power of CE to streamline CRISPR workflows with reliable reagent QC and a simple and accurate screening process while simultaneously elucidating the zygosity of positive clones.

> Learn more...


NGS library QC is essential to the generation of successful sequencing results. Several solutions have been developed to deal with the QC challenges of various types of NGS libraries, from short-read to long-read sequencing platforms, ChIP-seq, RNA-seq, and beyond.

> Learn more...

Genomic DNA

An accurate understanding of genomic DNA quality, quantity, and size is important for numerous methodologies including evaluating isolation success and NGS. Methods of evaluating the quantity, quality, and size of gDNA exist, though many are unable to reliably resolve challenges associated with genomic DNA analysis.

> Learn more...

PCR Fragments

Determination of amplicon size and concentration is a crucial aspect in post-reaction analysis of PCR. Traditional methods of PCR fragment analysis lack the sensitivity and resolution demanded by many applications.

> Learn more...


Active in myriad biological processes, RNA is the target of many applications, from microarrays to NGS. With diverse types of RNA, small RNA, mRNA, rRNA, and more, unique analytic challenges are posed. Several solutions for the quantification, qualification, and sizing of RNA samples have been developed, though many do not fully address the analytic challenges.

> Learn more...


Cell-free DNA (cfDNA) is of increasing interest to clinicians and researchers alike as a promising biomarker for various disease states. cfDNA requires rigorous assessment of quality prior to use in NGS workflows to ensure successful sequencing results.

> Learn more...

Large Fragment DNA

The advent of next-generation long read sequencing and synthetic genomics has increased interest in large DNA fragment analysis. Ideal for QC steps in the SMRTBell library workflow from Pacific Biosciences®, the large fragment DNA kits for the Fragment Analyzer can quantify and qualify DNA fragments and smears through 50 Kb.


Commonly employed in plant genetics, TILLiNG (Targeting Induced Local Lesions in Genomes) is a reverse genetics approach used to discover small and point mutations, such as SNPs. Detection of TILLiNG induced mutations depend on heteroduplex assays.

> Learn more...

Plasmid DNA

Assessment of the amount of supercoiled plasmid DNA in a sample is a critical measurement for many applications, such as: purifications, DNA vaccines, and gene therapy products. The Plasmid DNA Analysis Kit (DNF-940) delivers high quality sizing and relative quantification of supercoiled plasmid.

Commonly analyzed nucleic acid samples include:

  • NGS Libraries (Illumina and PacBio)
  • Plasmid (supercoild and linear)
  • SSR/Microsatellites
  • PCR Amplicons

Technical Information


The 5400 Fragment Analyzer brings parallel capillary electrophoresis with fluorescent detection to automated, high-throughput workflows. Integration of the 5400 Fragment Analyzer into automated workflows is largely dependent on the powered sample drawer, and the ability of the sample drawer to interface with a robotic arm.

Diagram Parallel Capillary Electrophoresis Array

The 5400 Fragment Analyzer has a single sample drawer that holds a standard 96-well plate. Samples are separated using a 96 capillary Short (33-55) or Long (55-80) capillary array. Electrodes adjacent to individual capillaries provide the appropriate voltage for electrokinetic injection of sample into the capillaries. After injection, a constant, appropriate voltage is applied to separate injected nucleic acids. At the detection window, the capillaries are arranged in parallel, passing through the optical platform.

Nucleic acid detection is accomplished with a rigorously designed optical platform comprised of an LED light source (470 nm excitation), camera lens, and CCD detector. Fluorescent light passes from the LED through the array window. The emitted fluorescence from the intercalating dye then passes through the camera lens and specific band pass filters spatially imaged onto the CCD detector. This system enables real-time detection of nucleic acid separations.


Instrument Sample Plate Capacity1 Plate or 96 Samples
Minimum Sample Volume20 µL (2 µL of sample typically required for dilution)
ResolutionAs low as 3 bp (gel dependent)
Sizing AccuracyNormally 5% or better (size dependent)
Sensitivity<50 pg/µL for smears <5 pg/µL for fragments
Light Source PowerSingle 1,000 mW LED
LED Wavelength470 nm
Emission Collection DeviceCCD detector
Software5400 Fragment Analyzer System Software, ProSize Data Analysis Software
Data Export FormatMicrosoft© Excel spreadsheet
Environmental ConditionsIndoor use, standard laboratory environment, 20 - 23°C
Relative Humidity Range<80% (Non-condensing)
Electrical100 - 200 VAC; 50 - 60 Hz; 15A
DimensionsMass: 38.5 Kg (85 lbs)
Size: H x W x D = 61 x 35 x 51 cm (24 x 14 x 20 in.)
CertificationsCertifications, Certified by the CSA group

Reagent Kits

Quantitative Analysis Kits

Reagent kits below are for sizing and quantitative analysis, using internal standards for accurate quantification.

DNA/NGS Fragment Analysis
Large Fragment Analysis
Genomic DNA Analysis
RNA Analysis

Qualitative/Sizing Analysis Kits

Kits below are for sizing and qualitative analysis, using a double injection of sizing markers and sample. Appropriate for genotyping or analysis of SSR's, microsatellites, and PCR fragments.

TILLiNG/Mutation Discovery Kits

Miscellaneous Parts and Components (contact your sales person for more details)

  • (A1300-033) Modified Bottle Cap for 50mL Conical Tube
  • (A1300-034) Modified Bottle Cap for 250mL Conical Tube
  • (A1300-036) Buffer/Waste Tray Carrier
  • (M1300-025) Tray Carrier - Standard
  • (F1300-109) Tray Carrier - Fully Skirted Tray
  • (F1300-107) Tray Carrier - 12 vial strip (0.2 mL)
  • (P60-20) Fragment Analyzer 96-Well Buffer/Waste Tray
  • (P60-22) Fragment Analyzer Waste Tub
  • (FS-SMO15) Mineral Oil Dropper Bottle, 15mL
  • (GP-440-0100) Capillary Storage Solution, 100 mL

Capillary Arrays

Capillary arrays are the core of the 5400 Fragment Analyzer affecting all aspects of electrophoresis. The array cartridges are robust, with a long lifetime, providing high quality, automated separations of nucleic acid samples. Current capillary array offerings include:

Array length is provided in centimeters with two numbers. The first number is the effective length of the capillaries - the region of the capillary that observed for separation - while the second number describes the overall length or the length of the capillary from end to end. The number of capillaries in each array directly impacts throughput, the more capillaries per array, the more samples that can be run in parallel. Array length affects both the speed of the separation and upon the separation resolution. A shorter array will provide faster electrophoresis times, while a longer array will increase separation resolution.

As a dedicated high-throughput instrument, the 5400 Fragment Analyzer utilizes only the 96 Capillary Arrays, available in Long (55-80) and Short (33-55) lengths. Other arrays would compromise the capability of the instrument to serve as a nucleic acid analysis powerhouse.

Use the capillary array-kit matrix below (separation times provided in minutes) to identify which capillary array is best suited for each unique application and level of throughput.

Separation times are reported in minutes.
Quantitative Analysis
NGS LF Genomic RNA
DNF-473 DNF-474 DNF-477 DNF-464 DNF-492 DNF-493 DNF-467 DNF-487 DNF-488 DNF-470 DNF-471 DNF-472
96 Capillary Short 50 50 40 55 50 50 50 50 50 22 40 40
96 Capillary Long 80 80 80 80 80 80 70 70
Separation times are reported in minutes.
Qualitative TILLiNG / CRISPR
DNF-900 DNF-905 DNF-910 DNF-915 DNF-920 DNF-930 DNF-935 DNF-910T DNF-920T DNF-910CP
96 Capillary Short 60 60 45 50 50 30 20 50 50 50
96 Capillary Long 80 80 70 80 80 75 35 80 80
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