An electrospray ionization interface incorporating an electrodynamic ion funnel has been designed and implemented on a linear ion trap mass spectrometer (Thermo Electron, LTQ). We found ion transmission to be greatly improved by replacing the standard capillary–skimmer interface with the capillary–ion funnel interface. An infusion study using a serial dilution of a reserpine solution showed that ion injection (accumulation) times to fill the ion trap at a given automatic gain control (AGC) target value were reduced by ∼90% which resulted in an ∼10-fold increase in peak intensities. In liquid chromatography tandem MS (LC–MS/MS) experiments performed using a global protein digest sample from the bacterium, Shewanella oneidensis, more peptides and proteins were identified when the ion funnel interface was used in place of the standard interface. This improvement was most pronounced at lower sample concentrations, where extended ion accumulation times are required, resulting in an ∼2-fold increase in the number of protein identifications. Implementation of the ion funnel interface on a LTQ Fourier transform (FT) mass spectrometer showed a ∼25–50% reduction in spectrum acquisition time. The duty cycle improvement in this case was due to the ion accumulation event contributing a larger portion to the total spectrum acquisition time.