Its general questions also about the quality of results between the two methods?what about the total protein ID?for example if I performed the two methods for 2 protein mixtures, in one of the mixtures we expect much proteolysis due to proteases, in this case, is there a difference regarding protein ID?
We published a paper last year that used both of these techniques together. In general, they are complementary -- they each see different elements of the same sample. That said, Top Down -- particularly quantitative high throughput top down -- has a steep learning curve.
Article Integrated Bottom-Up and Top-Down Proteomics of Patient-Deri...
The simple answer: From the specific to the general, and from the general to the specific, respectively.
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