CHEM 146C Experiment 5 Measuring Gas phase Basicities of Amino Acids using an Ion Trap Mass Spectrometer Yat Li Department of Chemistry Biochemistry University of California Santa Cruz Objective In this laboratory experiment we will learn 1 The principle of mass spectrometry MS 2 How to perform MS and MS MS analysis 3 How to measure the gas phase basicities of amino acids using MS MS technique Mass spectrometer Ions with different mass to charge ratio m z can be separated and analyzed by mass spectrometer mv2 zV Hzv mv2 r m z H2r2 2V m mass of the ion z charge of the ion H applied magnetic field r radius of arc of deflection V applied accelerating voltage Ionization methods 1 Electron impact method electron M e M 2e 3 Fast Atom Bombardment atom 2 Chemical ionization method ions NH4 RH RH2 NH3 4 Electrospray for marcomolecules such as proteins Instrumentation of mass spectrometer Single focusing MS Double focusing MS Quadrupole MS Time of Flight MS Determination of molecular mass of ions An acidic solution containing two amino acids Amino acid A Phe Amino acid B Leu Phe H MS Spectrum Phe H Leu Leu H Ion separation and analysis using MS MS technique AHB ions are separated and further analyzed by MS MS MS MS Spectrum Phe H Leu H Kinetics in the fragmentation of ions At equilibrium AH B kf kb BH A G RTefflnkeq AH B k1 k2 AHB proton bound dimer At equilibrium k1 AH B k2 AHB k3 k4 and G free energy of the process R ideal gas constant Teff effective temperature at ion dissociation keq equilibrium constant BH A k3 AHB k4 BH A keq k1k3 k2k4 BH A AH B Kinetics in the fragmentation of ions keq k1k3 k2k4 AH B BH A k1 k4 k1 and k4 refer to collision rates between ions and neutral molecules keq k3 k2 G RTefflnkeq RTeffln k3 k2 RTeffln k2 k3 The ratio is equal to the product ratio which is to a good approximation equal to the ratio of the intensities for these two ions in the MS MS spectrum AH B k2 AHB k3 BH A G RTeffln AH BH