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CHEM3013 Mass spectrometry Workshop/Assignment 2

Q1. You want to analyse a peptide solution by positive (sample A) and negative (sample B) ion MS. To facilitate ionization, to which samples do you add ammonia and to which sample acetic acid? Why is NH3 and not NaOH added? (0.5 marks)


Q2. Why are the peptides from a tryptic digested protein typically single charged in ESI-MS? Compare to peptides from a protein digest with the OmpT protease. (1 mark)


Q3. Give the relation between the ion velocity and the accelerating electric potential difference.

(0.5 marks)


Q4. Calculate the time of flight (tTOF ) for a proton (mass=1.6726•10-27 kg; charge=1.6022•10- 19 C) that was accelerated by an electric potential difference of 1000 V and is travelling in a field-free  region of length 2 m. (0.5 marks)

Q5. Repeat the calculation from Q4 with molecules of masses 1000 Da and 1001 Da and draw conclusions on the required acquisition speed of the detector. (0.5 marks)

Q6. Below are the full scan MS spectrum (upper panel) and the MS/MS spectrum of the double charged ion at m/z=740.7 Da (lower panel) of a tryptic peptide obtained from bovine serum albumin. Also           indicated are the y-ions (upper row) and a short series of b-ions. Identify the peptide. (1.5 marks)



Mass of a peptide is the sum of peptide units + H +OH

m = Si    + mh 2o


Q7. Describe the ions that are produced when a peptide is fragmented in low energy collision. (1.5 marks)

Q8. Describe an application where targeted mass spectrometry using an inclusion list might be used. (1.0 mark)

Q9. Briefly explain how iTRAQ works. (1.5 marks)

Q10. Give two reasons why in DXMS analyses the protein is digested with pepsin. (1.5 marks)