Troubleshooting HPLC Pressure Fluctuation Problems (Unstable Baseline)

Few things in chromatography are more frustrating than dealing with large pressure fluctuations (>1% ripple). If the pump pressure is unstable, and fluctuating up and down, then it will negatively impact your ability to analyze, measure, and integrate sample peaks in a reliable manner. A smooth, flat baseline is needed to run and develop methods, collect the data (peaks), integrate, and report the reproducible results. Baseline instability during an analysis may lead to the entire analysis being declared invalid.

So what causes the HPLC pressure to sometimes fluctuate in a wild manner up and down on your HPLC system? Unfortunately, many things... Most result from poor training, and incorrect operation techniques, but some are maintenance-related so be sure and keep your chromatograph in excellent condition. Maintain a logbook for each instrument and record what types of maintenance and service have been performed over time, with the date and list of parts used/replaced. Additionally, maintain a preventative maintenance schedule (e.g. every six months) to inspect and clean the entire HPLC system to check condition, verify operation, and minimize unproductive downtime.

HPLC Pump or System Pressure Fluctuation Causes and Solutions:

Air/gas in the Liquid or Mobile phase (Failure to Degas Mobile phase or Loose fittings)

• Air gets into the system due to a leak or from gas trapped in the mobile phase. Find and correct the cause of the leak and/or degas the mobile phase (use continuous Vacuum degassing or a Helium sparging system only).
• Leaks are the most common cause of instability, but insufficiently degassed solution is a close second. Make sure your degasser is working 100% correctly (they require professional servicing every 5 years). HPLC pumps require a degassed mobile phase for reliable operation.

Loss of Prime. Improper Priming of the System

• Failure to flush ALL of the lines with freshly degassed mobile phase, before use (every day), will often result in all kinds of instability problems until all of the old gas-filled mobile phase has been purged from the system.
• This could take many column volumes of liquid. Make sure you account for any vacuum chamber volume too. Properly prime the pump heads before use.

Sticking Check Valve(s)

• If air is exiting the pump outlet, the pump will not function properly. Both Inlet and Outlet valves should be inspected. Remove and clean the check valve(s). Be sure the pump is fully primed with liquid as the check valve might just have an air bubble in it (common on Waters, Thermo, and Shimadzu systems). 
• Sometimes sonication of the valve for ten minutes in a beaker containing warm solvent does the trick (e.g. MeOH or IPA/Water). Though very rare, ACN has a bad reputation for polymerizing in solution. If the system has sat unused for a long time OR was not properly flushed out when last used, particulate matter may clog the flow path.
• Small sticky particles may form (ACN polymerization) and cause the check valve to stick inside the housing (use fresh, filtered solvents only to prevent these problems). Clean and inspect any suspect valve first. Replacement of the check valve may be needed in some cases to restore operation.

Note: This problem of "sticking" check valves is most likely to be an issue in HPLC pumps with mechanical (gravity or spring) check valves with ruby balls, not modern style active inlet check valves ("AIV") which are electromechanical (solenoid valves) and are very reliable, much less susceptible to these problems. In any case, verify the operation of all valves while under pressure (back pressure is needed for them to function correctly).

Worn Pump Piston Seals

• Commonly observed as rapid up/down spiking on all channels and an inability to maintain or produce backpressure (the pump will often prime with no problem, as this is done at low pressure).
• Run a formal pump high-pressure leak test at max pressure to confirm (remove the column and replace it with a calibrated backpressure restriction line for all testing).
• Clean pistons and replace piston seals to repair (you should have spare pistons and seals on hand).
• Seals are a maintenance item so expect them to wear out and need regular replacement.

ALSO READ: Tips and Advice for Preparing your HPLC Pump

Flow rate is too low (may be inappropriate for the system)

• Running at a flow rate that is below the optimum range of the specific instrument (i.e. System rated for 200 to 2,000 μL/min, but run at 100 to 200 μL/min or at the limit of the range) may result in an unstable baseline.
• The cause may be due to pump cavitation, loss of prime, or non-optimized piston stroke volume.

HPLC System Back Pressure Too Low

• To maintain prime in the system. Most types of analytical HPLC systems require a minimum system back-pressure of 40 or more bars to maintain enough pressure (mechanical compression) on the component parts to run reliably. 
• Too low a pressure often results in a loss of prime, cavitation, mixing problems, turbulence, and poor reproducibility. Correct sizing of a column, particle size, flow rate, and mobile phase composition should all take into account achieving enough back-pressure on the system to maintain a stable baseline throughout the entire analysis.
• Monitor the system back-pressure at all times for stability. High-quality research-grade HPLC systems are often capable of maintaining stable isocratic flows with less than 1% ripple and 0.2% ripple common ("ripple" is a term we often use to describe the pump's pressure output over time relative to the baseline (S/N)).

Mixing Problem (Gradient or Isocratic Online Mixing)

• If your active mixer or proportioning valve (AKA: Gradient valve) is defective or dirty, then one or more of your mobile phase channels may not be getting to the pump.
• Air would most likely be mixing with the mobile phase causing the unstable flow. Clean or replace the valve.

Note: Always try flushing the gradient valve with pure IPA, then DH20 for about twenty minutes. This sometimes restores operation by wetting and flushing the internal seals (which may dry out).

Wrong Pump Solvent Compressibility Settings

• In HPLC we routinely subject different liquids to very high pressures which can result in measurable liquid compression. The degree of actual compression for each liquid varies, but the modern HPLC pump can compensate for this to improve the accuracy of the mixing and flow delivery.
• Most pumps provide for user adjustable solvent compressibility values. If the value input varies a great deal from the actual liquid in the system, then it can result in pressure fluctuations.

Example: Water has a value of 46, but Methanol is 120. Using the wrong value can cause instability.

Poor Solubility, Mobile Phase

• Sometimes the mobile phase that has been prepared (or mixed online) is not 100% soluble. This could be due to an inorganic salt additive that has not gone into solution or failure to fully mix and filter the mobile phase before use. Ultrasonication, a bit of heat, and stirring for 20 minutes can help to get everything dissolved.

Dirty inline filter

• A fouled or partially plugged filter can disrupt the normally smooth flow into a turbulent one. Some are installed as part of the pump (i.e. HP/Agilent brand pumps) and should be changed out every month (Yes, for the PTFE frit, replace it once a month with a new one).
• Other systems use these pre-filters downstream of the pump before the injector. Clean or replace all filters frequently. If used in your system, these are regular maintenance items and should be part of a general 'PM' program.

Dirty Solvent Pickup Inlet Filters

• These can become obstructed or fouled over time (esp. if used with aqueous solutions!). Just as with any built-in filter, the multiple solvent inlet pickup filters should be cleaned or replaced regularly to prevent particulates or any material that may contaminate or restrict the flow path from entering the system. 
• Mobile phase pickup filters are often 10 to 20 um and connect to the bottom of the low-pressure (e.g. Teflon) solvent lines in each bottle. If you use 316 Stainless steel filters (recommended for organic solvents), they should be removed, cleaned in an ultrasonic bath, rinsed, and replaced monthly.
• If you use sintered glass or other disposable type filters (often used with aqueous solutions), they should be disposed of regularly and replaced with new ones (replacement, not cleaning is recommended because sintered glass can not be sonicated and should be disposed of to prevent bacterial, mold or fungal contamination).
• A quick way to check if one filter is causing the pressure to fluctuate is to remove the filter from the one line, and then re-test the system. If the problem goes away, then returns when you re-install the filter back on the line, the filter may be obstructed (replace it),

The above list includes some of the most common reasons for unstable baselines. Other non-pump-related causes would include a bad/old detector lamp(s) or contaminated mobile phase. To find the cause, test and verify the operation of each component part of the HPLC.

Troubleshooting Advice: Test one part at-a-time, before moving to the next part. Never assume anything, test, re-test and verify or prove at each step.

ALSO READ: SOP for Operation and Cleaning of HPLC Pump