1. Overview of Mass Spectrometry
Sermin Tetik, PhD
Marmara University
July 2015, New Orleans

2. An overwiev What is the mass spectrometer?
What can mass spectrometers identify?
What are the different types of mass spectrometers?
Peptide fragmentation
Databese searching
Practical applications of mass spectrometry

3. What is a mass spectrometer
A. It measure mass
B. It can give information about chemical structure

4. 1. Sample preparation
2. Ion source
Generates ions
3.Mass analyzer
Separates ions
4. Detector
Mass spectrum
5. Analysıs

6. John B. Fenn Koichi Tanaka

7. The mass-to-charge ratio is often referred to as m/z and is typically unitless
m: the mass number (atomic mass/U)
z: the charge number (Q/e)

8. -Drug discovery
Determine structures of drugs and metabolites
Screen for metabolites in biological systems
-Clinical testing
Perform forensic analyses such as confirmation of drug abuse
Detect disease biomarkers (e.g. newborns screened for metabolic diseases)

9. -Geology
Carbon Dating
-Environment
-Residual gases
-Trace contaminants and toxins
-Test water quality or food contamination

10. B. Proteomics
Identification of biological material (proteins, nucleic acids, lipids)
Determine protein structure , function, folding and interactions
Detect specific post-translational modifications throughout complex biological mixtures
Quantitate (relative or absolute) proteins in a given sample
Monitor enzyme reactions, chemical modifications and protein digestion

12. A. Top-down proteomics: Identification of intact proteins

13. B. Bottom-up proteomics: Identification of intact proteins

14. B. Bottom-up proteomics: Identification of intact proteins

15. Top-Down VS Bottom-up proteomics:

16. Top-Down (+) Access the complete protein sequence
Abilty to locate post translational modifications (PTMs)
Time consuming protein digest is eliminated

17. Top-Down (-)
Complex spectra obtained limits approach to single protein or simple mixtures
Does not work well with proteins > 50 kDa

18. Bottom-up (+) Most widely used approach for proteın ID
Reverse phase HPLC provides high-resolution separation of peptide digests
Can analyze very complex mixture

19. Bottom-up (-)
Only a fraction of the total peptide population of a given protein is identified (loss PTMs identified)
Loss of information about low abundant peptides is mass spectra dominated by high abundance species

20. What are the different types of mass spectrophotometers?
A. MALDI(Matrix assisted laser desorption/ionization)-TOF (Time of flight)
B. LC/MS-MS

21. A. MALDI(Matrix assisted laser desorption/ionization)-TOF (Time of flight)

22. LC/MS-MS

23. Peptide Fragmentation by MS/MS

24. Peptide Fragmentation by MS/MS

25. Database Searching by MS/MS

26. Database Searching by MS/MS

27. Database Searching by MS/MS

28. Database Searching by MS/MS

29. Practical applications for mass spectrometry

30. Identify purified complexes to generate protein-protein interaction

31. Identify purified complexes to generate protein-protein interaction

32. Identify purified complexes to generate protein- protein interaction

33. Thank You