Autotune failed in LC 1290/MS 6490

Question

Hi Community, 
 We recently started working with LC-MS and due to inexperience we used a method with phosphoric acid in the mobile phase. We noticed a loss of sensitivity in the instrument and the autotune was not working. We have cleaned the entire source and followed Agilent's step-by-step tips for improving autotune, but the autotune still fails. The message "Coarse Tune Quad: Failed" shows and autotune not finished. The check tune finished. We change the calibration solution too. 
 Searching in other forums we saw that phosphoric acid can contaminate the MS and persist even after the source has been cleaned. 
 What can we do to resolve this issue and get back to work?

m4esti · Answer

Hi LGCMS200819,

Phosphoric acid contamination in an LC-MS system is a significant issue because it is not compatible with mass spectrometry due to its involatile nature , meaning it can form precipitates at the LC-MS interface, significantly reducing sensitivity by disrupting the electrical fields required for ionization and ion transfer.

Flush your HPLC system with copious amount of Milliq water and flow it to a waste container not the MS. In the MS, cool down the source, wipe with 80/20 IPA water solution. Rebuild the nebulizer with a new needle. Replace the glass ion capillary. For that you will need to vent. You might consider replacing the Peek tubing from switching valve to MS. This should get you started.

Autotune failed in LC 1290/MS 6490

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