Application of FR-ICR mass spectrometry in study of proteomics, petroleomics and fragmentomics

Chapter 1 introduces the concept of mass resolving power, mass resolution and mass measurement accuracy, the principle of the FT-ICR instrument for mass measurement, ionization methods, factors that control the mass measurement accuracy of FT-ICR MS and utility of high mass accuracy for analysis of biological samples and complex mixtures.;Chapter 2 describes the application of high mass accuracy for distinction of N-terminal and C-terminal electron capture dissociation/electron transfer dissociation (ECD/ETD) product ions of c and z based on their number of hydrogen plus nitrogen atoms determined by accurate mass measurement, and forms a basis for de novo peptide sequencing.;Chapter 3 presents an idea that at sufficiently high mass accuracy, it is possible to distinguish phosphorylated from unmodified peptides by mass measurement alone. We examine the feasibility of that idea, tested against a library of all possible in silico tryptic digest peptides from the human proteome database.;In chapter 4, we implemented dual electrospray ionization ETD on a custom-built 9.4 T FT-ICR MS. Two separate electrospray emitters are automatically switched for injection of positive (analyte) and negative (reagent) ions. Decarboxylated 2-(fluoranthene-8-carbonyl) benzoic acid is the ETD reagent anion. A linear octopole ion trap is the ETD ion/ion reaction chamber, and an RF voltage is applied to the front and back ion trap electrodes to confine both cations and reagent anions for ETD, after which the c- and z- type product ions are passed to the ICR cell for high resolution and mass accuracy analysis.;Chapter 5 describes a calibration procedure in which accurate masses of spacings from any two same type neighboring fragment ions differing by one amino acid residue are used to calibrate ECD and collision activated dissociation (CAD) MS/MS spectra of standard peptides with different molecular weights and charge states.;In chapter 6 all possible closest mass doublets (0