Nano electrospray combined with a quadrupole ion trap for the analysis of peptides and protein digests

A nano electrospray (NanoES)/ion trap combination was developed to take advantage of the long spraying time of the NanoES source (Wilm, M. S., Mann, M. Int. J. Mass Spectrom. Ion Processes 1994, 136, 167-180) for extensive experiments on the ion trap. The low flow rate associated with the NanoES allows for optimization of experimental conditions and data acquisition for more than 30 min with 1 µL of solution. Thus, even time-consuming experiments, such as multiple fragmentation steps or the sequencing of many components in a mixture, can be performed with very small volumes of sample. Stored waveform inverse Fourier transformation (SWIFT) signals were used during the injection period to accumulate ions of low intensity and to improve the dynamic range of the quadrupole ion trap. To sequence peptides, a combination of nozzle-skimmer fragmentation, SWIFT accumulation of a single fragment to high intensity, and a second fragmentation step was employed to obtain complete sequence information. Unseparated peptide mixtures were infused and weak portions of the spectrum were enhanced by using the SWIFT method, followed by fragmentation of various accumulated peptide ions.