Hej Everybody. I am looking for to get answer how many 2DE gels I have to run for a pilot study in clinical proteomics? Should I pooled the sample and run three 2DE-gels or just run 3 good 2DE-gels and run western-blot on the potential biomarker? How high the fold changes should be for quantification to be real? I read different paper and some reported more than 1.5 fold change etc. The best value is not 2 fold changes?
Merci,
Kambiz
If you pool the samples and run replicate gels, your biological n value is one. You would be better off running each sample separately. Even at that, a biological n of 3 may not be sufficient. You will know more after having run the gels and analyzed the results.
You need to do your experiments in biological and technical triplicates. More than 2 fold change in intensity of protein spots is recommended as significant.
I would suggest to run 3 samples in 3 2DE gels and use 2.0 fold as cut off, and validate differential spots using western in more samples.
TX everybody. Can anybody refer me with reference about 3 run samples and 3 2DE gels?
Merci,
Kambiz
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