Baseline Noise in Parallel Capillary Electrophoresis Data

Answer

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

Issue

One or more electropherograms have baseline noise.

Background

An example of baseline noise is shown in Figure 1.

Figure 1. Unexpected peaks and baseline noise in a ZAG DNA Analyzer electropherogram caused by bubbles in the reservoir.

Steps to Follow

There are several causes of parallel capillary electrophoresis baseline noise:

• Bubbles in the lines or reservoir can cause unwanted spikes. From the reservoir, the bubbles enter the capillaries. Prime the reagent bottle lines to remove the bubbles as follows: Ensure that there is adequate volume of each reagent in the bottles in the instrument side compartment (approximately 2.5 mL is required to prime a line). In the controller software, select Utilities > Prime. Select the fluid lines and select Okay to prime the lines. 
• The gel-dye mix may be contaminated with particulates. To clean the lines, use the prime command to flush the lines with 0.5N NaOH followed by de-ionized water. Then replace the gel bottle, Conditioning Solution bottle, and buffer plate with new plasticware and make new gel-dye mixture.  
• The sample or ladder may have become degraded or contaminated. Prepare a new sample or ladder aliquot.
• The capillary array window may be dirty. How to check and clean the capillary array window is described in the article How to Clean the Capillary Array Window on Agilent Parallel Capillary Electrophoresis Instruments.
• Does the signal from any of the capillaries look like background noise? Check the capillary alignment and try restoring the capillary performance as explained in the article No Data From One or More Capillary on Parallel Capillary Electrophoresis Instruments. 

After considering the preceding troubleshooting steps, run another separation to check if the baseline has improved. If these steps have not helped, contact Agilent support. To find the correct contact, go to the Contact Us page and choose your country.

Learn how to effectively maintain your Agilent Fragment Analyzer, Femto Pulse, or ZAG DNA Analyzer system: 5200, 5300 and 5400 Fragment Analyzer system manual on Agilent.com Femto Pulse user manual on Agilent.com ZAG DNA Analyzer system manual on Agilent.com

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

PR7001-3105