I have run 2D DIGE gels, done the statistic analysis, and ID by MS several spots of potential interest.
I have realized that I have several spots with the same ID, which I expected, more or less, due to the existence of isoforms and post translational modifications.
My problem which I would appreciate your help is:
How can I interpret the ratios obtained from the comparison of the images between treatments.
I have realized that in one treatment I have a high positive ratio for a spot Identified as a specific protein, and also the same identification (other spot) for a very negative ratio…
If some of the isoforms are induced during the sample treatment, such as urea, how can I believe the ratios for a specific protein… I mean, Can it happen that for a treatment I could have created more of an isoform and for the other treatment more of another isoform???
Thank you for your help
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