1. Molecular Mass Spectrometry

2. 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

3. Components of Mass Spectrometer
MS - Components
Components of Mass Spectrometer

4. GC/MS System Components

5. 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

6. MS - Ionization Desorption Ionization (105 D):
Field Desorption (FD) – High- potential 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

7. 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)

8. MS – Electron-Impact Ionization

9. MS – Ionization Chamber

10. MS – Ring Component Spectrum

11. MS - Spectra
CH2Cl2
MW=84
1-Pentanol
MW=88

12. MS - Chromatogram

13. MS – Isotopes Abundance
Most Other Percentage (%)
H1 H
C12 C
N14 N
S32 S S
Cl35 Cl
Br79 Br
Si28 Si Si

14. MS – Effect of Ionization Mode on SpectraEI
Field Desorption
Field Ionization
Glutamic Acid
HOOC-CHNH2 -CH2 – CH2 - COOH

15. MS – Ionization Mode and Spectra
Electron- Impact
1- Decanol
MW = 158
Chemical Ionization

16. MS – Chemical Ionization
Most often use reagent is CH4:
Electrons will form several ions: CH4+; CH3+; CH2+
Reactions (MH – sample molecule):
CH4+ + CH CH5+ + CH3
CH5+ + MH MH2+ + CH4 (M + 1)
CH3+ + CH C2H5+ + H2
C2H5+ + MH M+ + C2H6 (M – 1)
(M + 29)

17. GC/MS – Jet Separator

18. GC/LC/MS Sample Transfer

19. MS – Direct Sample Introduction
External Sample Introduction System
Direct Sample Probe

20. MS – Mass Analyzer Resolution: R = m/Dm
Where: m – mass of the first peak
Dm – difference between two adjacent peaks
Commercial MS have resolution 500 to 500,000
Dm = m/R

21. MS Analyzer – Magnetic Sector

22. MS – Electromagnetic Analyzer

23. Quadrupole MS Analyzer

24. MS – Quadrupole Filter

25. MS - Ion Trap Analyzer

26. MS – Time of Flight Analyser

27. MS – Reflectron Time of Flight Analyzer

28. MS – Fourier Transform Analyzer
Ion Cyclotron Resonance
Magnetic Field

29. GCMS - Instrumentation

30. MS - Instrumentation

31. LCMS – Electrospray Ionization (ESI)

32. MS – Capillary Electrophoresis

33. MS – Supercritical Chromatography

34. MS – Ion Detector

35. MS/MS

36. MS/MS Instrumentation

37. MS - Cost

38. Mass Spectrum
MW 240
5-Ethyl-5n-hexyl barbituric acid

39. MS - Chromatogram

40. MS - Quantitative SIM – single ion monitoring Spectra mode
Precision – 2% to 10%

41. 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)

42. 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

43. MS - Applications