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Troubleshooting

When should I use quadrupole versus ion trap isolation?

Quadrupole isolation is faster because ions must travel through the quadrupole analyzer regardless of the analysis type chosen. As a result, there is little to no time penalty when using the quadrupole for MS2isolation. In such a case, quadrupole transmission efficiency will depend on isolation width, m/z, and the cleanliness of the analyzer. Ion trap isolation is best suited for MS3 experiments, including those performed using multinotch isolation for TMT analysis; these types of isolation events are not possible with the quadrupole analyzer.

Is an ion routing multipole (IRM) the same thing as an HCD cell?

Yes. The ion routing multipole has multiple functions. The IRM not only functions as a collision cell for HCD fragmentation, but also as an ion storage-routing device so ions can be routed to the linear ion trap and back to the Orbitrap via the IRM cell.

If I am using ETD for proteomics, do I need to calibrate in negative ion mode?

Yes. The fluoranthene radical anion will need the calibrated ion optic and ion trap parameters for effective transmission and trapping for ETD.  

When do I do a calibration check and when do I actually calibrate?

Start by checking each group of calibrations, one at a time. If they fail the check repeatedly, perform calibration.
If any coarse calibrations are performed, the main calibrations must be performed as well.
Upon instrument install, the instrument needs to be calibrated.
Venting/replacing hardware/cleaning, the instrument needs to be calibrated.

Does the order in which I move through the calibration scheme matter?

Yes. The calibrations are designed to start with the ion optics and conclude at the ion trap. Subsequent calibrations rely on the previous ones being calibrated correctly. In particular, if anything other than mass is recalibrated, pAGC will have to be recalibrated. If eFT is calibrated, then mass must also be recalibrated. 

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