Exercise PMF1: hints
The protein is Epoxide hydrolase 1
To begin with, try a search of the whole of SwissProt with no modifications, 1 missed cleavage, and a mass tolerance of 0.5 Da
Data are m/z values from MALDI, so charge state will be MH+
- What is a suitable mass tolerance?
Having found a match, set the mass tolerance wide and then look at the error graph in the Protein View report. The error graph will also indicate whether a fixed tolerance (Da or mmu) or a proportional tolerance (% or ppm) is most appropriate
- What is the optimum setting for missed cleavages?
Try settings of 0, 1, 2, etc. and see which gives the highest score
- Is there evidence for Met-Ox?
Try including Oxidation (M) as a variable modification. Does the score get better or worse?