Skip to main content

How to clean an ACQUITY UPLC using Acid / base cleaning protocol after severe PEG contamination or other contamination? - WKB16167

Article number: 16167


If an ACQUIY UPLC is contaminated with PEG due to bad solvents, then the background stays visible. Even if the switch is made to good solvents, the PEG background stays visible on sensitive mass spectrometers like Vion, Xevo G2-XS, and Synapt G2-Si. Also if spectral peak fronting is observed on intact monoclonal antibody analysis on e.g. BioAccord (RDa) or Vion this protocol can be used. 

This protocol can of course also be used for other contaminants.

This procedure describes how to clean the ACQUITY according to the acid / base cleaning protocol.


  • ACQUITY UPLC H-Class (bio)


Remove the UPLC column and replace for a union.

  1. Purge line A and B for five minutes per line with cleaning solvent (see below).
  2. Purge FTN 60s for needle wash, 40 cycles for sample syringe.
  3. Create an analysis or sample list and run 20 injections of 10 microL of the same solvent as is running on the machine. Runtime one min, flow rate 0.8 mL/min on A1:B1 50:50. Direct the LC flow to waste and not to the mass spectrometer.

    Use the following cleaning solvents in this order:
    1) Magic mix (water-ACN-MeOH-IPA 25:25:25:25, v/v/v/v, with 1-2% FA)
    2) 10% ammonia in water (N.B. flush with water in between the acid and base flushes- steps 1 and 2)
    3) 10% ammonia in water (on channel A) and 100% IPA (on channel B).
    4) 100% IPA


The 10% ammonia solution really needs to be the final concentration. So if a stock of 28-30% ammonia is available it is only a 3 times dilution. Due to the very intense smell use a fume hood to prepare and additionally take good care when placing the bottle on the machine. 

Flush with water between the acid and base washes (steps 1 and 2)

Do not use this protocol on M-class. The PeekSil and silica tubings cannot handle a pH this high.

Not able to find a solution? Click here to request help.