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 distribution for the matched mass values.
(In Aldente, follow the Biograph link, in Mascot, click on the protein accession, in Profound, click on percent coverage.)
The error distribution 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?
Return to exercise page
|