Shutting down after a buffer run

Buffer salts dissolve in water. They can come out of solution when they meet organic solvent, or when the water dries away. Most of this guide follows from that.

If buffer is sitting in the pump, the column or the detector cell when the flow stops, the water slowly leaves and the salt stays. It stays as a solid, in parts machined to tight tolerances.

The Waters ACQUITY operator’s guide puts it plainly: buffer left in the detector can precipitate and damage the instrument.

What you do depends on how long the instrument will stand.

flowchart TD
    A["Buffer run finished"] --> B{"How long will the<br/>system stand?"}
    B -->|"Less than 24 hours"| C["Keep pumping the<br/>starting mobile phase"]
    C --> D["Lamp off"]
    D --> E["Slow the flow to a few<br/>tenths of a mL/min"]
    E --> F["Detector on, column heater<br/>at working temperature"]
    B -->|"More than 24 hours"| G["Lamp off"]
    G --> H["Flush the buffer out<br/>with water"]
    H --> I["Column and flow cell<br/>in 100% organic"]
    I --> J["Pump in 20% methanol<br/>in water"]
    J --> K["Power off, or column heater<br/>off or at 40 °C"]

Less than 24 hours

You don’t need to flush anything out. The goal is to keep the column ready for tomorrow.

1. Keep pumping the starting mobile phase through the column. That keeps the column equilibrated, so retention times stay the same.
2. Turn the detector lamp off. It saves lamp hours.
3. If it’ll be a few hours before the next injection, lower the flow to a few tenths of a mL/min. That saves solvent.
4. Leave the detector on, and keep the column heater at its working temperature.

If your software runs a shutdown method, check that it won’t start while you mean to leave the system running. In Empower it’s set in the instrument method.

More than 24 hours

Now the buffer has to come out.

1. Turn the detector lamp off.
2. Flush the buffer salts and additives out with water.
3. Flush the column and the flow cell with 100% organic solvent.
4. Turn the system off. If you’d rather leave it on, turn the column heater off or set it to 40 °C.

The pump needs its own flush. After a buffer, Waters says to wet-prime the pump with at least 5 system volumes of HPLC-grade distilled or deionised water.

If the pump will stand for more than a day, flush it with 20% methanol in water, not plain water. Plain water can grow microbes. Waters also says to change 100% aqueous mobile phase daily, and that about 10% organic in it prevents microbial growth.

Water first, then organic

Don’t go straight from buffer to organic.

When you switch from a strong buffer to an organic solvent, Waters says to flush the system well with distilled water before the organic goes in. Otherwise buffer and organic meet inside the flow path, and the salt can come out right there.

The same rule applies when you start up again. Before you put a buffered mobile phase back on the column, the Waters column manual says to flush it with water and organic at the same or lower organic content as the buffered mobile phase.

The plunger seals and the wash solvents

Seal wash. Salt from the high-pressure side can get pulled past the plunger seals and dry on the plungers. The seal wash keeps the plungers wet and washes that salt away. Waters says to prime the seal wash after any buffered mobile phase, after the pump has stood for a few hours, and if it has run dry.

Two rules go with it: don’t use a nonvolatile buffer as the seal wash, and don’t recycle the seal wash.

Wash solvents. Don’t put buffer in the weak wash, the strong wash or the needle wash. The operator’s guide says this more than once.

One number to keep

Waters says to keep nonvolatile buffers at or below 100 mM, to avoid salt precipitation.

What this protects

Salt can end up in a seal, a check valve, the flow cell or the column, depending on where it settles. On a Waters Alliance 2695, two of the parts in its path are the check valve cartridge and the plunger assembly. Chromkit supplies both. Lamp hours are the other thing a shutdown saves, and the lamps are here.

Sources

• Waters ACQUITY UPLC System Operator’s Guide, 71500082502 rev F: shutting down for less and more than 24 hours, the buffer-in-detector caution, seal wash, wash solvents, and appendix C on solvents (5 system volumes, 20% methanol, 100 mM, daily aqueous change, water before organic).
• Waters ACQUITY and ACQUITY Premier Columns Care and Use Manual, 720008980: the flush before a buffered mobile phase.

These are written for a Waters ACQUITY. Salt behaves the same on any system, but flush volumes are per system, so use your own instrument’s numbers where they differ.

Checked 3 October 2026.