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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
½ 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
DG = -RTefflnkeq
AH+
+ B
k1
k2
AHB+
(protonbound dimer)
At equilibrium, k1[AH+][B] = k2[AHB+]
k3
k4
and
DG: 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
D(DG) = -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
D(DG) = RTeffln([[AH+] / [BH+])