1. Mass Spectrometry

2. How is MS Done?

3. Basic MS Instrumentation

4. Magnetic Sector Mass Analyzers

5. Quadrupole Mass Analyzers

6. Reflector Time Of Flight

7. 3D Quadrupole ion trap Linear Quadrupole ion trap 3D radio-frequency ion traps: ions are trapped in center point (single point) 2D Linear trap: rf field is zero along the whole central line of the electrode configuration Quadrupolar ion traps (Paul trap)

8. 3 sets of parallel plates in a uniform magnetic field In a 7-Tesla magnetic field an ion with m/z =100 will spin 1,000,000 cycles (travel ~ 30 km) in a 1 sec. observation period Fourier transform ion cyclotron resonance (FTICR) MS

9. Linear trapping quadrupole FTICR

10. Mass Analyzers Instrument Mass analyzer2D trapQTOFFT-ICR/Orbitrap Mass accuracy500 ppm10 ppm1 ppm Resolution1,00010,000100,000 Sensitivity0.1 fmol1 fmol0.1 fmol Dynamic range1005010,000 Price$250K$450K$600K

11. Electron Impact Vs Chemical Ionization

12. Electrospray Ionization

13. Electrospray Vs Electron Impact

14. Proteins/Preteomics

15. Matrix Assisted Laser Desorption Iionization (MALDI)

17. Resolution/Sensitivity/Mass Accuracy Mass Mass Difference 5000 is typical unit resolution up to mass 5000 Proteins: 100 AA M = 15,000 R = 15,000 for unit resolution

18. Exact Mass/Mass Defect/Isotopic Abundance C 3 H 8 O 60.05754 C 2 H 8 N 2 60.06884 C 2 H 4 O 2 60.02112 CH 4 N 2 O 60.03242 R > 5300 required

19. base peak molecular ion Fragment isotope patterns The Mass Spectrum

20. Isotope Patterns CO 28 100 1.12 0.2 N 2 28 100 0.76 0.001 C 2 H 4 28 100 2.23 0.01 M+1 M+2 M

21. Fragmentation

22. Alkanes

23. Cyclic Alkanes

24. Alkenes

25. Aromatics

26. Alcohols

27. Phenols

28. Aliphatic Ethers

29. Aromatic Ethers

30. Ketones

31. Aromatic Ketones

32. Aldehydes

33. Carboxylic Acids

34. Esters

35. Lactones

36. Thiols