Deuterium Exchange
6
parameters may be easily controlled. In addition to auto-ionization, overfilling the trap decreases
mass resolution. Ion traps have an automatic mechanism for controlling the number of ions in the
trap, called automatic gain control, or AGC. The system does a pre-scan to determine the signal
strength and then adjusts the hold time in the trap to avoid filling the trap with too many ions.
The pre-scan signal is compared to a target ion count. The hold time is adjusted to match this
target. If there is insufficient sample to meet the target, the hold time is increased. However, for
very low sample concentrations the hold time may be impractical so a maximum hold time is
specified to avoid slowing down the data rate unduly. To avoid auto-ionization, the target ion
count and the maximum hold time may be decreased. For example, the default target ion count is
25000 and the default maximum hold time is 25000 us. To avoid auto-ionization the target ion
count can be decreased to 500 and the maximum hold time in the trap may be decreased to
2000 us or less. The method “” is set up in this way. Sample amounts can also be decreased to
cut down on the concentration of ions in the trap.
Another advantage of using decreased target ion counts and maximum hold times is resolution
is improved. The disadvantage of using decreased target ion counts and maximum hold times is
less sensitivity. Since ion trap mass spectrometers are about ten times as sensitive as quadrupole
mass analyzers, even when operating with decreased source controls, you can still have
comparable sensitivity to a quadrupole mass spectrometer.
How do you know if auto-ionization is a problem for your sample? Compare the mass spectra
on the leading and trailing edge of your chromatogram peak with the spectra near the apex. If the
M+1/M ratio changes drastically, with the spectra near the apex having much larger M+1/M
ratios, then auto-ionization is a problem. For approximate M+1/M ratios, you can then just use
the spectra from the leading or trailing edge.
Another way to tell if auto-ionization is a problem is to compare peaks in the spectrum. If your
compound has an even molecular weight, most of the fragment peaks will have odd masses.
Conversely, if your molecular weight is odd, most of the fragment ions will have even masses. If
you have good signal to noise, you should do another run with much smaller amounts of material.
However, to be careful, you should repeat your run with much smaller target ion counts and
maximum hold times, in addition to smaller amounts using the m50t200m12mw method.
Another indicator that auto-ionization is a problem is the appearance of a large number of
trailing peaks:
If your spectrum takes on this appearance, you need to dilute your sample by a factor of 50-100.
m/z
