Hi all,
I have limited experience in proteomics and would like your opinion.
I run proteomics analysis in three groups A: study group, B: first control of a disease with overlap with the study group, C: normal control.
The data analyzed by the proteomics team is the differential expression of A normalized to C, which is not what I want as there are some proteins that are also present in the relative quantification of B normalized to C.
Do you now how to control sample B so that I could identify only the proteins that are specific to A, excluding the common one in B?
Thanks you in advance
Clemence
Dear Clemence,
If I understood you correctly, I would recommend you to approach the proteomics lab and ask them to provide the original data where you probably will have all proteins expression in each sample in all groups. Having these data will allow you to perform any pair-wise comparison that you need.
If you have A normalized to C, and B normalized to C, then you can compare A and B and set a cut-off differentiating the two. This will work if it is quantitative setting.
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