Automatic identification of proteins with a MALDI-quadrupole ion trap massspectrometer

A matrix-assisted laser desorption/ionization (MALDI) ion trap mass spectro meter of new design is described. The instrument is based on a commercial F innegan LCQ ion trap mass spectrometer to which we have added a MALDI ion s ource that incorporates a sample stage constructed from a compact disk and a new ion transmission interface. The ion interface contains a quadrupole i on guide installed between the skimmer and the octapoles of the original in strument configuration, allowing for operation in both MALDI and electrospr ay ionization modes. The instrument has femtomole sensitivity for peptides and is capable of collecting a large number of MALDI MS and MALDI MS/MS spe ctra within a short period of time. The MALDI source produces reproducible signals for 10(4)-10(5) laser pulses, enabling us to collect MS/MS spectra from all the discernible singly charged ions detected in a MS peptide map. We describe the different modes of the instrument operation and algorithms for data processing as applied to challenging protein identification proble ms.