Loss of signal after use of different mobile phase on UPLC-MS/MS

I am currently running a method on our UPLC - Quattro Premier XE system with the following characteristics:Flow 0,3 ml of 0,1% formic acid/MeOH with a 4 min gradient using line A1 & B1. We are making use of the column manager.Now the following happened a few weeks ago:My colleague run his method with a flow of 0,3 ml of 10 mM NH4HCO3 pH10 using line A2 & B2 and had great resultsAfter this I ran my method again and had a loss of signal of appr. 70% when compared with the results I was used to.  Throughout the last weeks this turned out to be a very reproducible situation. His method with good results and my method with this enormous loss of signal when I ran my method after his method. Only after very extensive washing with 100% MeOH I got my high signals back. Now is my colleague's method a new one and I thought at first that the MS-part of the system was contaminated. Until recently. It was on one of my runs where I had high signals that I interrupted my series and primed the UPLC for 4 minutes with my colleague's mobile phase, the NH4HCO3 mobile phase so that he could run his samples directly after mine. Just priming, nothing more. Now I restarted my run and again had this loss of 70% of signal. And it stayed low until the end of my run. Now, during priming there is nothing going towards the mass spec so this must be a UPLC related issue. What is going on here?Is there anyone out there who knows what the problem is? Any suggestions? Would like to hear from you guys.Thanks you all.Bertrand van ZelstErasmus Medical Center, Rotterdam, the Netherlands


  • Bertrand

    Did you use the same column for both methods?

    Note you are switching from low pH to high pH



  • Hi Liz,

    Different columns.

    We are aware of the pH difference, but just priming the A2 line and resuming my run, I find it hard to imagine that just priming has that much of an influence.

    Best wishes,


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