Chapter Fourier Transform Ion Cyclotron Resonance Mass Spectrometry in the Analysis of Peptides and Proteins

Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry [1,2] has developed due to the fact that a charged particle in a uniform magnetic eld will undergo cyclotron motion, that is, will describe a circular path, perpendicular to the direction of the magnetic eld, and the frequency of that motion is inversely proportional to its mass-to-charge ratio. The technique of FT-ICR mass spectrometry offers the highest resolution and mass accuracy of all mass analyzers, making it ideal for the characterization of peptides and proteins. This chapter provides an overview of FT-ICR mass spectrometry and its applications in structural characterization of peptides and proteins. The principles of FT-ICR (ion motion, excitation/detection, and instrumental considerations) are discussed together with the features of FT-ICR that make it so suitable for peptide/protein analysis. Tandem mass spectrometry (MS/MS) techniques (sustained off-resonance irradiation collision-induced dissociation (SORI-CID), infrared 5.2.3 Infrared Multiphoton Dissociation (IRMPD) ................................... 133 5.2.3.1 Principles of Infrared Multiphoton Dissociation (IRMPD) ............................................................................ 133 5.2.3.2 Infrared Multiphoton Dissociation (IRMPD) of Peptides and Proteins ......................................................... 133 5.2.4 Blackbody Infrared Radiative Dissociation (BIRD) ........................ 134 5.2.4.1 Principles of Blackbody Infrared Radiative Dissociation (BIRD) .......................................................... 134 5.2.4.2 Blackbody Infrared Radiative Dissociation (BIRD) of Peptides and Proteins ......................................................... 134 5.2.5 Electron Capture Dissociation (ECD) .............................................. 135 5.2.5.1 Principles of Electron Capture Dissociation (ECD) .......... 135 5.2.5.2 Electron Capture Dissociation (ECD) of Peptides and Proteins .............................................................................. 135 5.2.5.3 Activated Ion Electron Capture Dissociation (AI-ECD) .......................................................................... 137 5.3 Hybrid Fourier Transform Ion Cyclotron Resonance (FT-ICR) Instruments ................................................................................................... 138 5.3.1 Quadrupole-Fourier Transform Ion Cyclotron Resonance (FT-ICR) ........................................................................................... 138 5.3.2 Linear Ion Trap-Fourier Transform Ion Cyclotron Resonance (FT-ICR) ........................................................................................... 139 5.4 Applications of Fourier Transform Ion Cyclotron Resonance (FT-ICR) in Proteomics ................................................................................................ 139 5.4.1 ‘Bottom-Up’ Approaches .................................................................. 139 5.4.1.1 Peptide Mass Fingerprinting .............................................. 139 5.4.1.2 Peptide Sequencing ............................................................ 140 5.4.2 ‘Top-Down’ Approaches ................................................................... 143 5.5 Summary ...................................................................................................... 144 References .............................................................................................................. 145 multiphoton dissociation (IRMPD), black body infrared radiative dissociation (BIRD), and electron capture dissociation (ECD) for the sequencing of peptides/proteins are described; see Section 5.2 for an explanation of these acronyms. The new generation of hybrid FT-ICR instruments are reviewed. Finally, the chapter includes a discussion of the applications of FT-ICR in ‘bottom-up’ and “top-down” proteomics.