Often when running pcr product we need to dilute the pcr product up to 1:80 to avoid too strong and broad a signal. At these dilutions the salt and bsa are too dilute to mahe a difference so I think that you should run the ladder without any additives except loading buffer and formamide if required rather than trying to make it look like a sample in its undiluted state

Always read "Instrument user manual" and try to find your trouble in the section "troubleshooting". I've found this information:

Broad or saturated DNA peak/band

a) DNA concentration

too high

Dilute the DNA solution in QX DNA Dilution Buffer.

Reduce the injection time.

Choose a method for high DNA concentration samples (e

Thank you both very much for your reply. I am running PCR products post amplification (30 cycles) of very low concentration of gDNA (around 5000 cells) and post cut of the PCR products with restriction enzyme. The restriction enzyme reaction is then stopped with an EDTA solution and the resulting cut product is run directly (without dilution) on the machine. My DNA concentrations are low, this is why I am not diluting my PCR products before running them on the machine.

I can try to dilute them, but the bands in the virtual gel view are already faint (Using L methods for low concentrated DNA on the machine). Do you suggest me to dilute them in any case to lower the concentration of salt/bsa/EDTA?

Huge thanks really for your help. No one in the department has ever used the machine and even if I am reading all the advanced user manual I am still struggling in setting it up.

As I know this type of machine can detect small concentrations. We use Bioptic Qsep that works the same way as Quiaxcel and I've never run undiluted product. Just test the proportion of the product and dilution buffer . Increase the injection time or choose a method for low DNA concentration samples.

Good luck!

The problem with electrokinetic sample loading is that the salts are small and highly charged so load first and the dna only loads later in the injection process and you get a weak signal due to low loading. Often this means that running the same sample twice may desalt the sample and it loads a lot better the second time. The other problem is that the ladder has a different salt concentration so loads early so sizing is an issue. If you cannot dilute the sample then you can precipitate and wash the dna and redissolve in water before preparing the sample for running or run the pcr mix through a disposable gel filtration column as used for cleaning up sequencing reactions