How to Clean the Capillary Array Window on Agilent Parallel Capillary Electrophoresis Instruments

Answer

This Information Applies To: 5200/5300/5400 Fragment Analyzer, Femto Pulse, and ZAG DNA Analyzer

Issue:

Dirt or dust on the capillary array window can cause baseline shifts or elevation of the baseline. Figure 1 shows an example electropherogram with baseline shifts. It is sometimes possible to see the dirt or dust in the View Capillary Positions screen in the Agilent ProSize data analysis software. This screen can be opened by clicking Analysis>View Capillary Positions in ProSize. An example of dust on a capillary array is shown in Figure 2.

Figure 1. A portion of a Fragment Analyzer electropherogram with Baseline shifts indicated with blue arrows.

Figure 2. Fragment Analyzer capillary positions from the View Capillary Positions window in ProSize. The capillaries are depicted as distinct blue peaks. Dust will show as additional signal, see right-most peak.

If the baseline shift or elevation has occurred in just one run, the instrument ventilation between runs may be sufficient to remove the particles. However, if the baseline shifts or baseline elevation persists for multiple runs cleaning the capillary array window can be a useful troubleshooting step.

Steps to Follow:

Caution: Be gentle to avoid damage to the capillaries or capillary array.

Open the side door and hood of the instrument.
Remove the light guide from the array window as shown in Figure 3.
Use a small nylon paintbrush or Kimwipe to gently clean the dust off the window while the window is dry. Brush across the window from left to right or right to left, not up and down. The window is highly fragile! Figure 4 demonstrates the capillary array window cleaning using a paintbrush on an Agilent Fragment Analyzer. The dust is typically on the capillaries due to static cling and can be removed easily with this step. If more intensive cleaning is needed, proceed to steps 4–9. Otherwise, proceed to step 10.
Remove the bundle end of the capillary array using the capillary array bundle removal tool. Place bundle in provided protective cover.
Remove the capillary array window from the capillary array window holder. Do not touch the array window.
Place a paper tower behind the capillary array window. An example of a Fragment Analyzer or ZAG DNA Analyzer capillary array window is shown in Figure 5 and a Femto Pulse capillary array window is shown in Figure 6.
Using a spray bottle filled with 70% isopropanol or ethanol solution, gently spray the capillary array window.

Use a small nylon paintbrush to gently brush the capillaries in one direction while they are still wet. Alternatively, a lint-free cloth can be used to blot the array window dry.

Caution: It is important to let the capillaries air dry before re-attaching the light guide. The light guide can evaporate the alcohol solution resulting in alcohol condensing on the glass filter behind the array window.

Reinstall the capillary array window, bundle, and light guide.
Perform a separation on the instrument. This separation should have sample, marker, or blank solution in every capillary position so that the file can be used to check the capillary alignment.
Check the alignment of the capillaries in the Agilent ProSize data analysis software. Click Analysis>View Capillary Positions. In the View Capillary Positions window, if the alignment is correct, the red dots will be at the top of each blue peak. If the alignment does not look correct, it is possible to drag and drop the red dots onto the top of the blue peaks. Once you are happy with the capillary alignment, click Accept to confirm the current capillary positions and return to the main ProSize menu. This will correct the alignment for this data file only.
If you had to adjust the capillary alignment for this separation, then it will be necessary to correct the alignment using the instrument controller software. Capillary alignment in the controller software will avoid the alignment being incorrect in future data files. Please check Chapter 4 of the Fragment Analyzer System Manual, Femto Pulse User Manual or ZAG DNA Analyzer System Manual for instructions. It is recommended and easiest to follow the Capillary Alignment from a File method. The capillary alignment should be done with the new data file, as only this latest run will have the current capillary positions.