5: Mass Analysis

This chapter on mass spectrometry (MS) provides a compact overview of the area from the basic fundamentals to key applications selected to give the best understanding and indicate the proper use of GC-MS instrumentation. We start with a historical perspective on mass spectrometry, which is followed by a section on the foundations of atom theory which introduces important terminology and the laws of nature (the origin of atomic and molecular mass, natural distributions of isotopes, the mass defect and the monoisotopic as well as the nominal mass of a given ion etc.). Subsequently, the reader finds condensed sections on MS instrumentation, in which the two most important ionisation methods (electron (impact) ionisation (EI) and chemical ionisation (CI)) and MS analysers (time of flight (TOF), linear quadrupole and quadrupole ion trap analysers) used for mass-to-charge value determination in GC-MS, are covered. Finally, we convey the fundamental principles of EI mass spectral interpretation. After a close look at the isotopic distributions found in the molecular ion region of EI mass spectra, we discuss the formation of characteristic fragment ions observed in EI mass spectra of exemplary organic compounds. The reader will be shown how to understand prototypical EI fragmentation pathways, which have been selected to exemplify how to identify, assign and suggest individual ion structures on the basis of EI mass spectra.