I use Bruker EVOC mass machine to analyze the MRM chromatograpgy of UDP. The shape of MRM peak was not smooth. (See the attachment) I have tried C18 and HILIK columns, mobile phase (ACN and Water) with or without formic acid. These changes didn't improve the shape of peak. Does anyone know how to smooth the shape of MRM peak?
That peak shape looks likes unstable spray in some ways, but your baseline seems fine. I'm assuming you've run controls and the system setup is okay? Another suggestion would be too much sample added, and you are saturating the system. The peak sides are almost vertical and it doesn't look like you are getting a gradual elution, that you see with a good peak, more of a sudden arrival. I assume you are monitoring other masses in the same run? If so, do they have a good peak shape?
Another possibility is the dwell time. How long are you acquiring data for on that particular mass? Again, if you've run standards, you should know the system setup is fine.
I certainly agree with all the comments above: standards, controls etc. However I wonder what gradient you do have. Your peak is 30 sec wide and it elutes at the 3rd minute. If we exclude the possibility that you have your materia eluting in the injection volume (and that your gradient or column do not work the way you suppose them to work and do not retain your analytes at all), then the gradient is obviously short. It can be either UPLC or fast LC. The only problem is that you would have much narrower peaks in both cases... So what are your LC conditions and injection volume? This can possibly explain some peculiarities of your peak: width, precipice-like front and back ends of your "peak". I am not sure about this oscillation, if it is overload I would rather expect stump-like form, but who knows...
Looks like a completely saturated peak to me- vertical sides and flat-topped at 20.000 cps according to the y axis. The oscillation might be down to the saturation behaviour of the detector - I am not familiar with the newer Bruker instruments unfortunately. Have you tried running a dilutions series rising in steps of 5, starting at 10e4 to 10e5 lower amounts injected? Is the peakshape still unstable if it has e.g. 500-1000 cps?
Thanks for all suggestions above. I have tried this experiment again lately. According to the suggestion from Bruker, I changed the "scan time" of mass machine to 2000ms. ( It was 50ms last time) Then the shapes of peaks became OK now.
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