3500xL Genetic Analyzer - FAQs

You can purchase a computer for installation of the secondary analysis software packages (e.g., Sequencing Analysis, GeneMappersoftware) 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.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

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.

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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.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

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.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

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.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

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 (https://www.thermofisher.com/content/dam/LifeTech/Documents/PDFs/3500-Start-Up-Procedures.pdf) or the Applied Biosystems 3500/3500xL Genetic Analyzer Getting Started Guide (Data Collection Software v.3.1)(https://tools.thermofisher.com/content/sfs/manuals/100031809_3500_3500xL_Software_v3_1_UG.pdf).

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 GeneMapperSoftware 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)(https://tools.thermofisher.com/content/sfs/manuals/100031135_3500_3500xL_DataCollection3_UB.pdf).

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

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.
- 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. A possible cause is septa that is old/re-used. Septa can become sticky and gummy over time and eventually start sticking to the array. In the 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. Worst case scenario is that the plate remains on array as the autosampler starts to move, bending the electrodes and breaking the array. We officially recommend that the plate septa be used one time only. Re-use of septa can result in contamination and sample degradation. However, we are aware that some of our customers will rinse the septa with water and re-use them. If choosing to re-use septa, do not use bleach, detergents, or solvents to clean the septa, it will cause them to dry out faster and risks contaminating the system.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

“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:

1. Valve stuck in open position
2. Large air bubble under the piston
3. Polymer:
-Wrong polymer type (e.g., instrument thinks it has POP-7 on it but it really has POP-4)
-Old/degraded polymer
4. 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.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

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 mentioned in the User Guide or in the Technical Note on Starting up the system (https://www.thermofisher.com/content/dam/LifeTech/Documents/PDFs/3500-Start-Up-Procedures.pdf).

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 have 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.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

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.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

A blinking red light on the instrument may indicate that a hardware component has failed or a possible communication disruption has occurred between the instrument and computer. Completely shut down the instrument, wait for 2 minutes, and then start up as documented in the Applied Biosystems 3500/3500xL Genetic Analyzers: Starting Up the Instrument(https://www.thermofisher.com/content/dam/LifeTech/Documents/PDFs/3500-Start-Up-Procedures.pdf) or the Applied Biosystems 3500/3500xL Genetic Analyzer Getting Started Guide (Data Collection Software v.3.1)(https://tools.thermofisher.com/content/sfs/manuals/100031809_3500_3500xL_Software_v3_1_UG.pdf).

If the instrument goes from a flashing amber light to red light, one or more of the hardware components has failed the hardware diagnostic, and a service call should be opened up.

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The initial software registration is performed with your Field Service Engineer during the instrument installation. Once the initial registration is done, you will need to renew the license annually. There is no cost associated with renewal, just a computer with internet access and email access.

For detailed instructions on renewing the license on the Applied Biosystems 3500/3500xL Genetic Analyzers: Renewing the Software License (Data Collection v.2.0, 3.0, 3.1) Technical Note (https://www.thermofisher.com//content/dam/LifeTech/Documents/PDFs/3500%20License%20Renewal.pdf).

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If we do not specify the expiry date or number of uses, the warranty will last for 12 months from the date of shipment.

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If you map the network drive so it shows up under Computer as a drive letter, then this feature can be configured from the Instrument Data Collection Software through the Results Group by going to the Destination tab, clicking “custom” and then browsing to the location on the network. For Applied Biosystems 3500 series Genetic Analyzers, additional steps will be required. Please contact Technical Support at techsupport@thermofisher.com for more information.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

The instrument computer can be connected to your local network via the second NIC card by your local IT group. We don't offer Technical Support to assist with networking issues, and our warranty and service contract terms exclude coverage for instrument system problems that are caused by the network connection (i.e., computer virus, hacking, updates, or patches that alter the compute environment). However, our field service team will respond during the warranty period and while the instrument is covered by an AB Assurance service contract to isolate the cause of any problem either with instrument hardware, software, chemistry, or that arises from an external environmental source including the connection to a customer-owned internal network. Beyond that we can escalate issues to a product technical team who can review instrument logs and advise on the nature of the problem in an effort to help customers find and correct the source of the problem.

For tips on connecting your computer to the local network, please see the Instrumentation Networking Technical Note (https://www.thermofisher.com/content/dam/LifeTech/Documents/PDFs/Instrumentation-Networking.pdf).

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All of our systems have been tested with NortonAnti-Virus Software.

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The Applied Biosystems 3500/3500xl Genetic Analyzer capillary arrays are warrantied for a specific number of runs or until the expiration date printed on the array package, whichever comes first. If you notice that you are starting to get reduced data quality (e.g., shorter reads, trailing peaks in all 4 colors) even with the Sequencing Standard, these may be signs that the array requires changing.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

Thermo Fisher Scientific can only provide warranty on performance on non-expired reagents. Using reagents past their expiration date is a risk and may compromise your data integrity.

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Putting the polymer back at 2-8 degrees C may extend the life of the polymer, however, we do not have any data indicating how long it might extend it. Removing the polymer and putting it back on the system can also result in a trade-off in usage. When placing it back on the system, you will need to degas the polymer for 30-60 min, refill the pump/block, array, and remove bubbles, which will cause you to use more polymer for maintenance than you would for running samples and may decrease the number of runs you can get out of a single polymer bottle/pouch.

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For the Applied Biosystems 3500 Series Genetic Analyzer, the buffer will keep for 14 days if room temperature is <25 degrees C and for 7 days if >25 degrees C.

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For the Applied Biosystems 3500 Series Genetic Analyzer, the polymer can remain on the instrument for 14 days if room temperature is <25 degrees C and for 7 days if >25 degrees C.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

Maintenance tasks on the Applied Biosystems 3500 series Genetic Analyzer are broken down into daily, weekly, monthly, and as-needed tasks. The Maintenance calendar in the Applied Biosystems 3500 series Data Collection Software can provide a monthly or daily view of tasks scheduled for the instrument. When a task is due to be performed, it will show up in the Dashboard view under Calendar Reminders. For detailed information on the maintenance steps and when to perform them, please refer to the Applied Biosystems 3500/3500xL Genetic Analyzers Maintenance Checklist (https://www.thermofisher.com//content/dam/LifeTech/Documents/PDFs/3500%20Maintenance%20Checklist.pdf) or the Applied Biosystems 3500/3500xL Genetic Analyzer Getting Started Guide (Data Collection Software v.3.1) (https://tools.thermofisher.com/content/sfs/manuals/100031809_3500_3500xL_Software_v3_1_UG.pdf).

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

The Data Collection and secondary analysis software requires certain permissions in order to function (Read, Write, Delete). To avoid issues with restrictions placed on user accounts, it is recommended that you log in either as Administrator or INSTR-ADMIN.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

There is no harm in restarting the system daily, but it should not be necessary unless there is an occasional loss in communication between the instrument and computer or the system is running significantly slower than normal. If the problems in run speed or communication loss are persistent, then it may be indicative of a larger problem. Technical Support should be contacted for further assistance at techsupport@thermofisher.com.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

We recommend that you perform a restart of the system once a week. The system may require a restart more frequently if you experience issues related to a communication interruption between the instrument and computer. Some systematic issues include:

-The software freezing or becoming unresponsive
-The run timer not counting down or flashing back and forth between two different times
-No data present at the end of the run

In the event of a communication issue between the instrument and computer, close the Data Collection Software (perform a forced shutdown of the application through the Task Manager if Data Collection is unresponsive), completely power down the instrument and turn off the computer. To properly clear the memory, power down the system for at least 2 minutes prior to a restart

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

After performing the short-term or long-term shutdown wizards:
1. Close the Data Collection program by clicking on the X in the upper right hand corner.
2. Press the power button on the instrument
3. Go to the Start menu and select Shut Down to turn off the computer (if the default shows “Sleep”, click the arrow next to it and select “Shut down”).

Step-by-step instructions for the shutdown procedures can be found in the Applied Biosystems 3500/3500xL Genetic Analyzers: Shutting Down the Instrument Technical Note (https://www.thermofisher.com/content/dam/LifeTech/Documents/PDFs/3500-Shut-Down-Procedures.pdf) and the Applied Biosystems 3500/3500xL Genetic Analyzer Getting Started Guide (Data Collection Software v.3.1)(https://tools.thermofisher.com/content/sfs/manuals/100031809_3500_3500xL_Software_v3_1_UG.pdf).

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

For the Applied Biosystems 3500 Series Genetic Analyzer, if the instrument will be idle for 1- 2 weeks, perform the short-term shutdown of the system. If the instrument will be idle for more than 2 weeks, perform the long-term shutdown using the Instrument Shutdown Wizard.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.

The Applied Biosystems 3500 Genetic Analyzer system includes both the instrument and the computer - you cannot start or restart one without starting the other. Improper boot sequence can lead to communication issues, aborted runs, and possible loss of data. The proper boot sequence is as follows:

1. Turn on the computer and press on Ctrl + Alt + Del, then OK to get to the login screen but do not log in.
2. Press the power button to turn on the instrument and wait for the green light.
3. Log in to the computer with the INSTR-ADMIN user account and wait for the Integration Service to launch. When all of the services in the Integration Service are on, a green checkmark will appear over the icon.
4. Wait 1- 2 minutes to allow for programs to load in the background and then launch the Applied Biosystems 3500 Series Data Collection Software.

Step-by-step instructions for the start-up procedures can be found in the Applied Biosystems 3500/3500xL Genetic Analyzers: Starting Up the Instrument Technical Note (https://www.thermofisher.com/content/dam/LifeTech/Documents/PDFs/3500-Start-Up-Procedures.pdf) and the Applied Biosystems 3500/3500xL Genetic Analyzer Getting Started Guide (Data Collection Software v.3.1)(https://tools.thermofisher.com/content/sfs/manuals/100031809_3500_3500xL_Software_v3_1_UG.pdf)

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Instruments Support Center.