We have Agilent 6460 LCMSMS system in our laboratory. Today, I encountered a strange problem with this instrument. The problem was it shows nice peak of an analyte during MS2 scan mode, precursor ion check mode and MS2 Sim mode whereas there is no peak in product ion scan as well as MRM mode. I am quite familiar with my method and all critical instrument parameters seem normal. The product ion scan as well as MRM were fine and the method worked prfectly fine just before 2-3 days. I suspect it as a fragmentation related issues but I am not sure. Collision gas flow and pressure also normal. Could anyone encountered such problems? Could you please help me to troubleshoot this strange problem?
Thank you in advance.