This assignment focuses on the methodology of peptide mass finger printing (PMF) and use of mass spectrum analysis software. The lecture notes provide a good foundation for this but you will have to carry out additional personal research to effectively answer the questions. The learning objective of the assignment is to give you an appreciation of the importance of bioinformatics and mass spectrometry in biomedical research technologies. Both mass spectrometry and bioinformatics are important skills in this area.
Please complete the following tasks:
The spectrum in the attached picture is a PMF profile obtained from a spot cut out of a 2 dimensional electrophoresis gel.
1) Identify the protein that produced the attached PMF mass spectrum, you may use any online resource to do this but I suggest the MASCOT server is a good place to start. The profile was produced using trypsin and is derived from a human cell lysate. List the amino acid sequence of each fragment.
2) The MASCOT server lists a number of chemical modifications for peptides. Which of these are likely to have occurred due to the electrophoresis used to isolate the protein? What effect will these have on the protein’s mass?
3) Using dot points, outline the processes used to produce the PMF profile starting from protein lysate.