1 CH908 Structural Analysis by Mass Spectrometry revision lecture. Prof. Peter O’Connor

2 Summary of the Lectures 1. Introduction lecture a. Understand ionization by EI, ESI, and MALDI b. Understand the primary types of mass spectrometers (Quadrupoles, Ion Traps, TOF, and FTICR) c. Understand how to extract elemental composition information from isotopic patterns. d. Understand the definitions of resolving power and mass accuracy. e. Understand that mass spectrometers measure mass/charge ratio, not mass, and how to determine the charge state. f. Understand the nitrogen rule, the R+DB calculation, and how they can be used to test if an ion is possibly the molecular ion.

3 Summary of the Lectures 2. Electron impact spectra a. Understand the nitrogen rule, the R+DB calculation, and how they can be used to test if an ion is possibly the molecular ion. b. How can the isotopic distribution give you information about elemental composition? i. How do you calculate the number of Cl, Br, O, S, Si atoms? ii. How do you estimate the number of Carbon atoms? iii. What about monoisotopic atoms like Na, Cl, Al? iv. What about metals? c. What are the rules for a molecular ion? What happens if you can’t find the molecular ion in a fragment spectrum? d. What’s the difference between an odd-electron and an even-electron ion? e. EI spectra: i. aliphatic/aromatic ii. alkane/alkene series. iii. characteristic ions (e.g. 30 Da) iv. anomalous even-mass fragments… v. The odd-even electron rule.

4 Summary of the Lectures 3. Electron impact spectra (continued) a. Where do we assume the charge starts? b. Primary fragmentation mechanisms in EI i. alpha cleavage ii. inductive cleavage iii. displacements iv. rearrangements c. Loss of the largest alkyl radical rule. Why does it work? d. Fragmentation patterns. i. alkanes ii. Aldehydes and ketones iii. hydroxides and sulfides e.McLafferty rearrangement. Why does it work? f.How can isomers be differentiated by MS?

5 Summary of the Lectures 4. Electrospray and MALDI (2002 Nobel Prize) a. How does electrospray work? Draw it. b.Main features of electrospray i. Very soft ionization method ii. multiple charging iii. even electron ions iv. most ion signals in the m/z range because of ii. v. most common method in modern MS labs. c. How to calculate charge states? i. isotopic spacings ii. charge state spacings iii. Addition of known modifications. d. How does MALDI work? Draw it. i. What lasers do we use and why? What matrices do we use? ii. What’s the most common instrumental configuration for MALDI? Why? e. Main features of MALDI. i. singly charged ions primarily. ii. even electron ions. f. Explain the peptide digest fingerprint experiment.

6 Summary of the Lectures 5. Tandem mass spectrometry (of peptides, mostly) a. What is tandem mass spectrometry? i. Why is it necessary to isolate ions first? What happens if you don’t do a good job at isolation? ii. What are the two main fragmentation methods? (CAD and ExD) iii. How does CAD work? (draw it) iv. How does ExD work? (draw it) b. Explain a selected reaction monitoring experiment. c. Explain a neutral-loss scan experiment. d. Know the Roepstorff/Biemann peptide fragmentation nomenclature. Be able to calculate the mass of ABC/XYZ fragment ions given a peptide sequence. e. CAD generates specific fragments with peptides, which? Are there any amino acids that influence fragmentation? Which? f. ExD (ECD, ETD, EID, etc) generates specific fragments for peptides, which? Again, is there any amino-acid specificity? How does it compare with CAD? g. Why do CAD and ExD generate different fragments for peptides? h. How can you distinguish leucine from isoleucine in peptides?