1. Mass Spectrometry Week 2 Lab S117 Fall 2011

2. Overview Post-Lab: Percent Alcohol in Wine – TurnItIn.com – Working with data sets – Analyzing data sets – Analysis of experimental procedure Pre-lab: Mass Spectrometry – Fragmentation – Protein Analysis Practical matters of lab meeting

3. Assignments Sign up for turnitin.com Formal reports due electronically up to time of lab One minute  24 hours late = 20pt penalty Give copy of lab notebook to AI in lab

4. Excel Working with data sets Statistical Analysis Certainty and uncertainty – Measurements – Experimental limit – Reproducibility

5. Experimental Design Practical Weaknesses? Propagation of Error Was the distillation useful?

6. Pre-Lab: Mass Spectrometry Analysis of isotopes!

7. Nominal Mass and Exact Mass Nominal Mass: Low resolution – 35 Cl = 35 Da – 37 Cl = 37 Da – CO = N 2 = 28 Da Exact Mass: High Resolution – CO = 27.9949 Da – N 2 = 28.0061 Da

8. Analysis of Molecules Parent peak (molecular ion)and fragment peaks Analysis of fragment patterns useful Application to Cl 2 caffeine isovaleraldehyde

9. Analysis of Biomolecules Complex molecules Molecular mass in kiloDaltons (kDa) Nobel Prizes for MS of proteins

10. Proteins Made of Amino Acids

11. Mass Spec and Mutations Sickle Cell Anemia Point Mutation How can MS be used to identify Mutations?

12. Identification of Proteins Comparison of 2D electrophoresis

13. Identification of Proteins Purified Protein Mix of Peptides Trypsin Digest Mass Data of mixture Mass Spec MS Library Identity of Protein ASRLVMKQQKD ASR LVMK QQK D Example 1 Example 2 ASRLVKMQKQD

14. Practical Matters Meet in chemistry computer lab 006 Mass Spec lab tours Dry lab: No special clothing requirements! Remember formal report and lab notebook