Applied Biosystems 3500/3500xL Genetic Analyzers Support—Troubleshooting

A perpetually blinking amber light usually indicates that there is a door open on the instrument or a bad door sensor. Open the main door, the oven door and the detector cell door (small black door with the laser warning on it) and close them again. After the autosampler stops moving the light should change to green. If the light does not go to green, it is possible that a door sensor is not working properly and a service call may be required. 

The reasons for this will vary depending on what version of Applied Biosystems™ 3500 Data Collection Software you are using:

For the Applied Biosystems™ 3500 Data Collection Software v.1.0, v. 1.1 and v.2.0, the TxnPassStore.dat file may have become corrupted. To fix:

• Right click on the Integration Service icon in the lower right corner of the screen and select “Exit”.
• Go to D:/Applied Biosystems/3500/webMethods/IntegrationServer/config
• Right click on the TxnPassStore.dat file and select “Restore Previous Version”
• Select the most recent version from before the problem started and click “Restore”. 
• When the roll back is complete, click OK and restart the computer and the instrument in the order in the User Guide or Technical Note on Starting up the system.

For the Applied Biosystems™ 3500 Data Collection Software v.3.0, v. 3.1, the Integration Service no longer relies on web Methods in these versions of Data Collection. Most cases of the Integration Service not launching has been tied to changing the computer name after the software was installed or upgraded. Changing the computer name back to its old name will resolve the problem. 

Some of the other causes of an Unstable Electrophoresis current detected error message are:

• Leak on the system
• Polymer that:
  • Has expired
  • Has been left on the instrument for more than the recommended time
  • Is a mixture of expired polymer and non-expired polymer
• Running Buffer that was:
  • Swapped with the water position on the Autosampler deck
  • On the instrument longer than 2 weeks 
  • Not filled to the fill line or evaporated below the fill line
• An arcing event that was not cleaned afterwards using the water wash wizard
• Not performing regular maintenance on the instrument
• Hardware issues

Inspect the system for leaks. If you do not see any leaks on the system, perform the wash the pump chamber and channels wizard using the conditioning pouch and place fresh, non-expired polymer and fresh Anode and Cathode buffer containers. If the problem persists, a service call may be required.

“Leak detected” error messages can also occur when the piston on the pump moves further than expected during the movement of the pump. The usual cause for this is a leak on the system, usually due to an improperly tightened or threaded fitting or a broken capillary. However, if this is not observed, some of the other reasons include:

• Valve stuck in open position
• Large air bubble under the piston
• Polymer:
  • Wrong polymer type (e.g., instrument thinks it has POP™-7 on it but it really has POP™-4)
  • Old/degraded polymer 
• Improper/no maintenance on the system

Inspect the system for leaks. If you do not see any leaks on the system, perform the wash the pump chamber and channels wizard using the conditioning pouch and place fresh, non-expired polymer and fresh Anode and Cathode buffer containers. If the problem persists, a service call may be required.

The location of the files is determined by the Results Group. Double check the Location tab in the Results Group selected for the run to make sure it has not been changed and the files saved to a different location. On the Applied Biosystems™ 3500/3500xL Genetic Analyzer, the location can also be determined in the File Naming Convention. If the Results Group was not assigned to the plate, then it’s possible the files are in the location in the File Naming Convention. 

Some other causes of missing data include:

• If the system is networked, and something interrupts the network connection then it might interrupt the connection between the instrument and the computer. For the Applied Biosystems™ 3500 Series Genetic Analyzers, if the Results Group and File Naming Convention were both pointing to the network drive to save the files, the samples will have to be re-run. 
• If the septa is old or re-used. We officially recommend that the plate septa be used one time only. However, we are aware that some of our customers will rinse the septa with water and re-use them. In those instances, the septa can become sticky and gummy over time and eventually start sticking to the array. In a best case scenario, the array will lift the plate off of the autosampler just enough to break the connection with the plate sensor and abort the run. The Event Log might show that the run aborted due to the user aborting it, so the run will appear to have completed or stopped with no errors and no data. Worst case scenario is that the plate remains on array as the autosampler starts to move, bending the electrodes and breaking the array. Replace the plate septa regularly (each run is recommended, but after no more than 4–5 rinses; do not use bleach, detergents, or solvents to clean the septa, it will cause them to dry out faster and risks contaminating the system). 

If the system has not been started in the last week, completely shut off the instrument and the computer, wait for 2 minutes and restart it as documented in the Applied Biosystems™ 3500/3500xL Genetic Analyzers: Starting up the Instrument Technical Note or the Applied Biosystems™ 3500/3500xL Genetic Analyzer Getting Started Guide (Data Collection Software v.3.1).

If the computer itself seems to be running slowly after restarting, you may need to defragment the hard drives. For the Applied Biosystems™ 3500 Series Genetic Analyzer, you can defragment the C and D drive only if the GeneMapper™ Software has not been installed on the system. 

If the system has been restarted and the computer slowdown is limited to the instrument Data Collection Software, it is possible that the database/data store is getting full. For the Applied Biosystems™ 3500 Series Genetic Analyzer, follow the instructions on Archiving and Purging the Data Store and other additional files found in this User Bulletin (even if you are not upgrading, the instructions still apply for general data store maintenance). 

On the Applied Biosystems™ 3500 Series Genetic Analyzer, the polymer pouch may not be sitting properly or the check valve may be stuck in the open position. Carefully detach the polymer pouch by pulling down the handle next to it, and then pull the handle up while guiding the pouch into place and secure it by pushing up on the plastic head of the pouch. If this fails, perform a wash on the system using the conditioning pouch. If reseating the tube/pouch and cleanup do not fix the problem, a service call may be required. 

If the array is stuck in the pump, even after loosening the knob, squirt around the edge of the array head with distilled water and try to remove it again. If the array will not move, a service call may be required. Do not use excessive force or tools to try and remove it. 

When placing the array on the instrument, the last step in the process is to loosen the array knob and the instrument forces any air bubbles around the array tip through the threading and the middle of the array knob. Some polymer gets pushed through as well and when it dries up, it appears as a white, flaky residue. Use a damp, lint-free cloth to remove it. 

Installation of the Data Collection Software for the Applied Biosystems™ 3500/3500xL Genetic Analyzer Data Collection Software is a complex process that requires a Field Service Engineer to install the software properly. 

You can purchase a computer for installation of the secondary analysis software packages (e.g., Sequencing Analysis, GeneMapper™ software) as long as the computer meets the software compute requirements (for processor speed, the minimum speed of the processor should be at least 3 GHz) and you can install the software yourself. 

For the instrument computer, the computer system has a much more stringent requirement and undergoes thorough testing to make sure it can handle the flow of data from the instrument to the computer. The images for the computer system are streamlined to make sure they have the proper drivers for the computer components, and the Operating System is optimized to make sure there is nothing running in the background that might slow the computer down, take up memory, or conflict with our software. Purchasing a computer commercially can introduce too many variables in terms of hardware and software that can negatively affect the data collection process so we cannot support connecting it to the instrument.