MALDI analysing my protein gave a MW 3% larger than the calculated size. Does anyone know why is that? I tried checking charges but still couldn't come up with a reasonable explanation. please help.
The MS operates with an accuracy at the 5 decimal sign. Can you provide m/z values in multiplication with corresponding standard deviations? A preferred temporal plot of the m/z should be also presented.
You can use this software: (http://proteowizard.sourceforge.net/tools.shtml).
3% sound like a fairly large addition (of course depending on the size of your protein), is it likely that your protein have any type of post translational modifications that would add to the theoretical weight?