Applied Biosystems 3500 - User Manual

Applied Biosystems 3500

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For Research Use Only. Not for use in diagnostic procedures.

Applied Biosystems

™

3500/3500xL Genetic

Analyzer

USER GUIDE

with 3500 Series Data Collection Software 3.1

Catalog Numbers 4405186, 4405187

Publication Number 100031809

Revision C

Table of Contents

Questions and Answers

A
Alejandra WalkerJul 28, 2025
Why is my Applied Biosystems 3500 polymer delivery pump so noisy?
- M
  Michael MosleyJul 28, 2025
  The polymer delivery pump (PDP) may be excessively noisy due to a couple of reasons. First, the array locking lever might not be in the correct position. Ensure it is locked correctly; if not, contact Thermo Fisher Scientific. Second, the polymer delivery pump block may not be pushed back into position after a capillary array change. Gently push the buffer-pin valve lever (yoke). If it doesn't move freely, restart the instrument and computer. If, after restarting, the lever still doesn't move freely, contact Thermo Fisher Scientific. Otherwise, push the upper polymer block all the way back against the wall.
S
samantha44Aug 5, 2025
What to do if Applied Biosystems 3500 autosampler doesn't move the plate?
- R
  Rick YoungAug 5, 2025
  If the autosampler isn't moving the plate, several factors could be at play. First, check that the plate retainer, plate (or tube strip), and plate base are assembled correctly, listening for a snap when clipping them together. If array tips are bent, replace the array. Also, ensure the plate base sits flat on the autosampler, with the pins aligned with the holes at the bottom and the sides latched. Securely clip the plate retainer and plate base together if the array lifts the retainer off the base. Finally, make sure the septum is fully inserted into position, listening for a click.
K
kari92Aug 11, 2025
What to do if Applied Biosystems 3500 has a power failure?
- T
  Timothy SnyderAug 11, 2025
  In the event of a power failure affecting both the instrument and computer, restart both the instrument and the computer.
J
Jeffrey MiddletonAug 19, 2025
What does blinking amber light mean on Applied Biosystems 3500?
- L
  Louis MendozaAug 19, 2025
  A blinking amber light on the front panel indicator of your Applied Biosystems Measuring Instruments means either the run is paused (resume run), or the instrument door is open (close the instrument door).

Applied Biosystems 3500 Specifications

General

Number of capillaries	8
Capillary Length	50 cm
Laser	Solid-state laser
Instrument Type	Capillary electrophoresis system
Technology	Capillary Electrophoresis (CE)
Weight	95 kg
Power Requirements	100–240 V

Summary

CHAPTER 1 Instrument and software description

Instrument and software description

Overview of the Applied Biosystems 3500/3500xL Genetic Analyzer and its software.

Instrument and computer requirements

Details on hardware and software specifications for the instrument and computer.

Instrument consumables handling, usage limits, and expiration

Guidelines for handling, usage limits, and expiration of instrument consumables.

CHAPTER 2 Start the system

Start the computer and instrument

Step-by-step instructions for powering on the computer and instrument.

Start the software

Procedure for launching the 3500 Series Data Collection Software.

Check system status in the Dashboard

How to verify system status, consumables, and calendar reminders.

CHAPTER 3 Set up and run

Prepare the instrument

Steps to ensure the instrument is ready for a run.

Create or import a plate

Instructions for creating new plates or importing existing ones.

Assign plate contents

Details on assigning samples, assays, and file name conventions to plate wells.

Prepare and load sample plates

Guidance on preparing sample plates and loading them into the instrument.

Load plates for run and create the injection list

Monitor the run

How to track the progress of an ongoing instrument run.

Check sequence or sample quality and re-inject samples

Methods for checking sample quality and re-injecting samples.

CHAPTER 4 Review sequencing results

Review results for the currently running sequencing plate

Review sequence quality

Evaluating the quality metrics of sequencing data.

Understand Quality Values (QVs)

CHAPTER 5 Review fragment;HID analysis results

Review results for the currently running fragment;HID analysis plate

Review sample quality

Evaluating the quality of fragment and HID analysis data.

Review sizing

CHAPTER 6 Run calibrations and install checks

Section 6.1 Run spatial and spectral calibrations

Procedures for performing spatial and spectral calibrations.

Section 6.2 Run an install check

Steps for running sequencing and fragment/HID install checks.

CHAPTER 8 Use Security, Audit, and E-Sig functions (SAE Module)

Administrators

Users

CHAPTER 9 Maintain the Instrument

Maintenance schedule

Overview of routine and scheduled maintenance tasks.

Clean the instrument

Install buffers

Replenish, change, flush, and store polymer

Maintain the pump

APPENDIX A Troubleshoot

Restart the instrument and the computer

Instrument troubleshooting

Common symptoms and causes of instrument issues.

Error messages

Explanation of common error messages and their solutions.

Dashboard troubleshooting

Software troubleshooting - general

Run, re-run, or re-inject troubleshooting

Resolving issues related to starting or re-running experiments.

Data;electropherogram troubleshooting

Troubleshooting issues with data quality and electropherograms.

Review Results troubleshooting

Link;load plate troubleshooting

Assign Plate Contents troubleshooting

Spatial calibration troubleshooting

Diagnosing and resolving spatial calibration failures.

Spectral calibration troubleshooting

Diagnosing and resolving spectral calibration failures.

Sequencing install standard troubleshooting

Troubleshooting issues with sequencing install checks.

Fragment;HID install standard troubleshooting

Troubleshooting fragment/HID install check failures.

Monitor Run troubleshooting

APPENDIX B Run modules and dye sets

Run modules

Dye sets

APPENDIX H Safety

Safety alerts on this instrument

Instrument safety

General safety precautions for operating the instrument.

Electrical safety

Guidelines for safe use of electrical power.

Laser

Chemical safety

Guidelines for safe handling of chemicals.

Biological hazard safety

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