This Information Applies To: 2100 Bioanalyzer system, 2100 Expert software
How to identify and troubleshoot late migration of the ladder, marker, and sample peaks in data generated on the Agilent 2100 Bioanalyzer system.
The ladder, marker, and sample peaks in the affected run take considerably longer to migrate compared to the peaks in the demo file of the same assay type. Late migration is usually accompanied by errors, similar to the ones shown in Figure 1. These errors indicate that the marker and ladder peaks are not detected after the anticipated number of seconds or not detected at all.
Verifying Late Migration:
With the analysis off, we would not anticipate the markers overlaying perfectly. However, clear delay in migration as shown in Figure 2 would be likely to cause problems with marker assignment.
Late migration can lead to peaks not being detected automatically and if the peaks don't migrate within the assays time window for detection they will not be detected at all. If the upper marker and all ladder peaks were detected, just not assigned correctly, then you may be able to still use the data by reassigning the upper marker as described in this Agilent Knowledge Portal Article. If the upper marker or biggest ladder peak is not detected, then accurate sizing or quantitation of the sample peaks is not possible.
Late migration caused by: Problems during chip priming, dirty electrodes, liquid spillage from the chip, loss of gel separation properties or the dye concentration being too high.
Steps to Follow
To prevent the unnecessary consumption of multiple chips during troubleshooting, please read this article in full and perform all recommended maintenance before running another chip.
To exclude a problem with the chip priming
Check the priming station base plate and syringe clip settings for your assay, especially if the instrument is also used to run other assays.
Perform the maintenance of the priming station. Instructions are located in chapter 9 of the Maintenance and Troubleshooting guide and in the Bioanalyzer how to video: priming station maintenance (Figure 3).
Exchange the silicone gasket if it hasn’t been changed for three months or if it shows any signs of damage or clogging. The part number of the new gasket kit is G2938-68716.
Visually inspect the priming station's syringe adapter for any indication of a blockage.
Prime and check the underside of the chip for any bubbles in the channels. Do not turn the primed chip upside down, rather check it by holding it up. In a properly primed chip, the microchannels will not be visible, the presence of bubbles would indicate a priming problem.
To exclude a dirty electrode cartridge
Caution: Make sure that the pin set is fully dry before placing it back into the electrode base. Even small amounts of liquid on the pin set can damage the high-voltage power supply. Before starting a run, run the short circuit test as described in chapter 4 of the Maintenance and Troubleshooting guide.
To exclude a problem with the chip preparation
To exclude a problem with the samples
Learn how to effectively maintain your Bioanalyzer:
Agilent 2100 Bioanalyzer System Maintenance and Troubleshooting Guide on Agilent.com