My intended AGC for full scan in Orbitrap (FTMS) = 5 x 10^5 and MS/MS scan in Iontrap (ITMS) 1x10^4.
Here my question is when I set up these AGCs do I leave the other parameters as default, by other I meant, in FT, the SIM and MSn should be left as it is? Likewise, in IT, the Full MS, SIM, and Zoom should be left as it is?
I have attached screenshots of the Injection control with my settings, do you think I have to change few parameters based on your experience.
FYI. I am analyzing phosphopeptides.
[Not important: In the ear of Solaris, I am still learning my mass spectrometry basics on an LTQ Orbitrap XL. Our mass spec runs by individual students here; mostly, we use our already established instrumentation methods. However, when it comes to a new experiment, it is difficult to get an expert opinion in person. ]
Hello Dr. Andreas,
Thank you so much for your quick response.
Yes, I am using 60K resolution. I was following several published articles on plant phosphoproteomics, where they used Orbitrap XL. Few of these articles used multistage activation; few did not. I was a bit skeptical about this; now I am feeling more confident to try out these settings you mentioned. I am running the pilot experiments for method optimization.
Regards,
Kamal
Kamal,
I support everything Andreas said here.
Make sure you also check the fill time settings to verify that they make sense. I've often seen them be whacky. You find them in the upper menu bar.
-ben
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