by
lmh » Fri Apr 13, 2018 12:22 pm
Haven't used an Orbi for a while, but do remember that the ion-trap Orbis have a mass range of only about one order of magnitude. If you get a nice signal on the low-res trap for heavy ions, but when you change to FT the heavy peaks disappear, it is this problem that you've encountered. If you only need heavy peaks, then increase the bottom range of your FT mass scans, and you will get better sensitivity at high mass. If you need high masses and low masses simultaneously, you may need separate scan events for low and high.
I may be completely wrong, someone correct me, but I believe this is a result of how the orbitrap bit is loaded with ions. In the LTQ-Orbi, the ions are first collected in a low-res trap and then injected, via the C-trap, into the orbitrap itself. Low-res traps cannot hold more than about a ten-fold range of masses at once. They need to apply an AC trapping voltage to hold ions in their quadrupole field, and if they apply too high a voltage, small ions will hit the quads and get lost. If they apply too low a voltage, the large ions won't be contained properly in the field. When doing low-res scans over a wide mass-range, I believe Thermo instruments actually do a couple of scans over smaller masses and stitch them together seamlessly to give you what you want (this is possible because the Thermo low-res traps are so fast). The orbi isn't so fast (because resolution is a function of dwell-time in the orbitrap, being an FT process), so it can't easily do two scans and join them without you noticing.
As I say, I might be completely and utterly wrong about this interpretation of the Orbi 10-fold mass issue, but the issue certainly was genuine last time I used an Orbi (which was, sadly, too long ago).