A hybrid radio frequency quadrupole linear ion trap-Fourier transform ion cyclotron resonance mass spectrometer

The subject of this dissertation is the development of improved instrumentation and methods for the analysis of peptides and proteins by tandem mass spectrometry (MS/MS). The first chapter describes the development and characterization of a proof-of concept realization of a new type of tandem mass spectrometer: a hybrid radio frequency quadrupole linear ion trap-Fourier transform ion cyclotron resonance mass spectrometer (RF QLT-FTICR). This tandem mass spectrometer configuration enables m/z isolation and dissociation of ions to be performed outside of the ICR analyzer cell in the confines of a RF QLT, where these manipulations can be performed quickly and efficiently.; The capability of the proof-of-concept hybrid QLT-FTICR instrument to provide real-time automated data dependent MS/MS analysis of peptides separated via high performance liquid chromatography, HPLC, was demonstrated by analysis of a complex mixture of peptides derived from E. coli. Diffusion limited extraction of ions from the QLT and the time of flight of ions from the QLT to the ICR cell were observed and characterized.; The second chapter describes the development of a new ion dissociation technique for peptide and protein ions: electron transfer dissociation (ETD). This technique is the ion/ion analog of electron capture dissociation, ECD. ETD can be implemented in RF ion trapping devices which cannot confine the thermal electrons required for ECD. Unlike CAD, ETD affords backbone cleavage of peptide ions without loss of labile modifying groups and provides more complete backbone fragmentation of large peptide and protein ions.; Extensive modifications were made to a RF QLT instrument including adaptation of a second ion source to provide the reagent anions. A dual RF trapping mode was developed to provide charge sign independent ion trapping in both the axial as well as radial dimensions of the QLT.; During reaction between multiply protonated peptide ions and anions, the partitioning between proton transfer and electron transfer reaction pathways was determined to be anion dependent. Reagent anions from anthracene and 9,10 diphenyl anthracene were demonstrated to react substantially by the electron transfer and induce ETD. The analytical utility of ETD was demonstrated with on-line MS/MS analysis of phosophopeptides separated via HPLC.