How to get differntial Protein expression from protein abundance?

Question

[Omar]

I have proteome data from MS that looks like this:

Accession   mock_2h DZ_2h   tZ_2h   iP_2h   cZ_2h
AT1G14640   414177.811  338580.8139 156843.029  0.01    429917.5057
AT4G04210   18772.64082 9343.005921 10221.41105 14003.91488 0.01
AT2G28210   1888.572701 3808.277547 5535.396042 3619.26865  0.01

So I've got the abundance for each Accession ID, that's how I received the data from collaborators but I want a package or a script to perform differential protein expression comparing treatment groups to the control, all the differential protein packages are starting with peptide quantification. If anyone knows a package that could do please let me know.

Thanks.

Answer 1

[mark.ziemann]

Hi Omar, consider transposing your data table so each row is a protein and each column is a sample. Assuming these values have already been normalised, you could run limma which is commonly used for differential expression of normal data.

[Saadyeh]

mark.ziemann Hi Mark,I have a similar question, but in my case, I have protein names and data for both a control and a condition group, each with three replicates. The data includes the number of proteins in each sample and they are not normalized. So for using Limma do I need to use log transform first? Is there other packages do better job or any resource that I can get more information is highly appreciated. I tried a few packages, they mostly need more data which I don't have. Thank you very much.