So I am doing my university junior research project which required to prepare and compare 2D gels containing proteins extracted from a bacterium (Sinorhizobium meliloti). These gels had the proteins seperated by isoelectric focusing. Now, some of the gels I had prepared had "train spots" on them and I am slightly confused by why they actually form. I know that these "train spots" form as a result of post-translational modifications but is that the only reason? Is there any association between their similar molecular weights & their differnt pIs that cause them to form next to one another?
Also, and more importantly, what about the phenomenon where protein spots of different molecular weight match predicted proteins (eg: they match to tubulin or an ATPase). I am confused as to what is happening there.
Any help clarifying the matter would be much appreciated thanks.