Our standard recommendation is to wash the syringes with 250 µL of 50 mM NaOH using the Syringe Wash utility between every run. This works well for cleaning the syringes the majority of the time.
If you experience run-to-run carryover that is not resolved by washing with 50 mM NaOH, the Syringe Wash utility allows one to wash with up to 6 different solutions which can cover a wide range of chemical space. For example, one can do high ionic aqueous washes at high and low pH, organic washes at high and low pH wash, and/or denaturing reagents (e.g. urea or guanidine) washes.
In the extremely rare cases where the approaches above do not resolve the issue, we have a couple of other options that can be tried but the approaches above address carryover in all but the most extremely "sticky" proteins. If you do run into this issue, please contact me or technical support to discuss other options.
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