Molecular Mass
Spectrometry
Mass Spectroscopy (MS)
 The elemental composition of matter of
samples
 The structure of inorganic, organic and
biological molecules
 The quantitative and qualitative
composition of complex mixture
 Isotopic ratios of atoms in samples
MS - Components
Components of Mass Spectrometer
GC/MS System Components
MS - Ionization
 Gas phase ionization (103 D):
 Electron Impact (EI) – Energetic
electron beam
 Chemical Ionization (CI) – Reagent
gaseous ions
 Field Ionization (FI) – high potential
electrode
MS - Ionization
 Desorption Ionization (105 D):
 Field Desorption (FD) – Highpotential Electrode
 Electrospray Ionization (ESI) – High
Electric Field (20 kV)
 Matrix – Assisted
Desorption/Ionization (MALDI)
 Plasma desorption (PD) – Fission
fragments from 252Cf
 Thermospray ionization (TS) – High
temperature
MS - Ionization
 Hard source – enough energy to rupture
bonds and producing fragments (EI)
 Soft source – provides always molecular
weight of the molecule (CI; ESI,
MALDI)
MS – Electron-Impact Ionization
MS – Ionization Chamber
MS – Ring Component Spectrum
MS - Spectra
CH2Cl2
MW=84
1-Pentanol
MW=88
MS - Chromatogram
MS – Isotopes Abundance
Most
H1
C12
N14
S32
Cl35
Br79
Si28
Other
H2
C13
N15
S33
S34
Cl37
Br81
Si29
Si30
Percentage (%)
0.015
1.08
0.37
0.8
4.4
32.5
98.0
5.1
3.4
MS – Effect of Ionization Mode on Spectra
EI
Field Desorption
Field Ionization
Glutamic Acid
HOOC-CHNH2 -CH2 – CH2 - COOH
MS – Ionization Mode and Spectra
Electron- Impact
1- Decanol
MW = 158
Chemical Ionization
MS – Chemical Ionization
• Most often use reagent is CH4:
• Electrons will form several ions: CH4+;
CH3+; CH2+
• Reactions (MH – sample molecule):
CH4+ + CH4
CH5+ + CH3
CH5+ + MH
MH2+ + CH4 (M + 1)
CH3+ + CH4
C2H5+ + H2
C2H5+ + MH
M+ + C2H6 (M – 1)
(M + 29)
GC/MS – Jet Separator
GC/LC/MS
Sample
Transfer
MS – Direct Sample Introduction
External Sample Introduction System
Direct Sample Probe
MS – Mass Analyzer
• Resolution:
Where:
R = m/Dm
m – mass of the first peak
Dm – difference between two
adjacent peaks
Commercial MS have resolution 500 to
500,000
Dm = m/R
MS Analyzer – Magnetic Sector
MS – Electromagnetic Analyzer
Quadrupole MS Analyzer
MS – Quadrupole Filter
MS - Ion Trap Analyzer
MS – Time of Flight Analyser
MS – Reflectron Time of Flight Analyzer
MS – Fourier Transform Analyzer
Ion Cyclotron Resonance
Magnetic Field
GCMS - Instrumentation
MS - Instrumentation
LCMS – Electrospray Ionization (ESI)
MS – Capillary Electrophoresis
MS – Supercritical Chromatography
MS – Ion Detector
MS/MS
MS/MS Instrumentation
MS - Cost
Mass Spectrum
MW 240
5-Ethyl-5n-hexyl barbituric acid
MS - Chromatogram
MS - Quantitative
 SIM – single ion monitoring
 Spectra mode
 Precision – 2% to 10%
MS – Spectra Interpretation
 Base peaks and Relative Ion Intensities:
 Determine molecular ion mass. CI if needed.
 Elemental composition from isotopic abundance:
 Look for A+2 pattern elements (Cl, Br, S, Si, O)
 Check A+1 ratios for absence/presence of S and Si
 Use the nitrogen rule to determine number of N’s (If
MW is even N=0 or even number. If MW is odd = odd
number of nitrogen atoms
 Estimate number of H, F, I, and P from isotopic ratios
and MW balance (P is multivalent; F=19; I=127 mass
units)
 Check allowance for rings and double bonds. Number of
double bonds or rings = x – 1/2y +1/2 z +1 (x=C, Si; y=H,
F, Br, Cl; z=N, P, O, S)
MS – Spectra Interpretation
 Use molecular ion fragmentation mechanism:
Check fragment masses differences for expected
losses (Cl = 35; Br=79; Me=15; Et=29 etc…)
 Look for expected substructures
 Look for stable neutral loss (CH2 == CHR)
 Look for products of known rearrangements
 Postulate structures:
Search library data base
 Run hit compound on the same instrument to
confirm
 Use MS/MS if further confirmation is needed
MS - Applications