- Two types of flushing techniques can be employed to reduce the damage caused by these salt buffers and extend the life of the system. Flushing the entire HPLC flow path and optionally, flushing the back of the pump pistons using a "seal wash" system.
(1) Flushing the HPLC Flow Path: Potential damage from salts can be avoided if you remember to always flush down the entire flow path of your HPLC each day (and anytime it may sit unused) with a proper mixture of HPLC grade water and some organic (to prevent the growth of 'critters'). Flush the column down first with an appropriate solution and then remove it from the flow path. Next flush the entire HPLC system down to rinse it of any remaining deposits (sometimes the column can be left in-line and flushed with the system. Consult your column manufacturer for advice). The exact mixture to use will depend on the exact type of mobile phase you are using. You want to select something which will dissolve the buffer used in your mobile phase into the solution plus incorporate some organic solvent component to reduce the surface tension and also deter the growth of bacteria over time. For example: A common Reverse Phase (RP) solution of 80% HPLC Grade water and 20% Methanol can be used in many applications. If you have an automated HPLC system, then this entire process can be stored as a "Flush" method and programmed to run at the end of each day's sequence or series of runs so you do not have to remember to do it manually.
(2) Seal Wash System Use: A second level of flushing buffers from the system involves the use of "seal wash" pump. These pumps are often small peristaltic pumps with silicone tubing connected to them (Some are simply gravity fed systems where the wash solvent bottle must be kept elevated and waste tubing kept low to function). The tubing is connected to a metal ring which surrounds the back of the main pump's piston in such a way that it can wash liquid over it and remove these deposits. When run with buffers, the main HPLC pump pistons receive a thin coating of the solution each time they complete a full stroke. Over time, the liquid evaporate and a film of buffer salts deposit on the sapphire pistons. These salts accumulate and can scratch the pistol surface allowing air to enter the system or leaks to results. Premature replacement of the pump head seals and pistons often results from this damage. Washing the internal flow path of the HPLC system (as described in section #1 above) does not wash away these salt deposits which occur outside on the piston surface. A "seal wash" system can be employed to assist to deal with the problem. The seal wash pump's inlet line can be placed in a bottle with fresh wash solution and through either an automatic timer feature set in the pump's software or through the operator manually turning the wash pump on and off, it can wash the back of the piston to remove these deposits. The solution used to wash the pistons will again depend on the type of mobile phase you are using (just like the HPLC flushing solvent). For most RP applications, I recommend a mixture of 80% HPLC Grade water and 20% Methanol. Other common seal wash solutions are: 90% HPLC Grade water and 10% IPA or 80% HPLC Grade water and 20% ACN. For most applications, I prefer using Methanol over IPA because it is much better at dissolving many of the buffers used. A third option would be to use a wash solvent which is the same as your mobile phase, but without any buffers added. Again, you must review your own method to determine which wash solution is best as their is no such thing as a 'universal' wash solution that can be used with all methods.
If you are running Normal Phase (NP) applications, then the seal wash can also be employed to keep the pistons 'wet' during operation and avoid excessive piston squeak noise which is common when running dry solvents (e.g. Hexane). Manufacturers often provide special piston seals designed for use with normal phase solvents, but sometime the incorporation of the mobile phase as a seal wash solvent can lubricate the pistons well. IPA can often be employed as a NP seal wash solvent choice too. In any case, always make sure that the silicone tubing used in your seal wash pumps is fully compatible with the wash solution you choose.