The first focus of the course is an overview of the subject and its history. The second covers the fundamentals of ionization to produce molecular ions. Ionization methods include electron ionization, chemical ionization, electrospray, and matrix-assisted laser desorption. Thermodynamic principles of ionization including ionization energies, proton affinities, and gas-phase acidities provide a fundamental basis for ionization. The third major focus is interpretation of EI and product-ion spectra from MS/MS. Mechanisms of gas-phase ion decomposition reactions, rates and thermodynamics of gas-phase ion processes, and ion-molecule reactions are discussed in terms of interpreting spectra. A major emphasis is the spectra of peptides and proteins, providing a basis for the field of proteomics and related "omics" areas. The fourth focus is the fundamentals of instrumentation design and implementation: quadrupole, time-of-flight, ion trap, orbitraps, and Fourier transform instruments. Combined or hyphenated GC/MS, LC/MS, and tandem mass spectrometry are also discussed. Applications in a variety of areas are worked in as the course progresses: structure determination of synthetic, natural products, metabolites, and biomolecules, exact mass measurements (high resolution MS), peptide and protein and other biomolecule sequencing, sensitive detection, trace analysis, and mixture analysis. Prerequisite: Chem 252 or permission of instructor.