Methods for cooling ions retained in an ion trap are described. In various embodiments, a cooling gas is delivered into a linear ion trap causing a non-steady state pressure elevation in at least a portion of the trap above about 8×10−5 Torr for a duration less than the ion-retention time. In various embodiments, the duration of pressure elevation can be based upon a period of time required for an ion to lose a desired amount of its kinetic energy.