I am using an un inoculated leaf sample and inoculated leaf sample with Phytophthora. So I want to see the deferentially expressed proteins in the inoculated sample when compared to the un inoculated; mainly the defense proteins. Is there any novel method using one dimension(SDS-PAGE) only....
It's going to be too crowded. You won't be able to isolate spots. It will be more like smears. If you use mass spec for identification, it will make the job much harder for your mass spec. You want to pre-separate as much as possible.
You might still get some hits of highly expressed proteins that ionize well, but you'll also be certain to miss lots of stuff that would be easy to see on a 2D gel.
Hi Vijesh,
You probably can use SDS-PAGE for comparative proteomics with limited results. Attached is an instruction of a 'teaching kit' for comparative proteomics. Muscle tissues from several different fish species are used for comparative proteomics by SDS-PAGE (see attachment). As you can see, protein band polymorphism is indeed observed at lower part of the gel (p.33-35). You probably can even cut out some bands for further analysis and find out what proteins they are. However, the bands on the upper part of the gel are too many to distinguish them. As John mentioned, they are too crowded. So, if you have to use SDS-PAGE and you are lucky, you might get some limited data. However, if you want to get a better and more comprehensive result, 2-D gel should be used.
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