I have two questions

1) I have few questions which I want to know if it is possible to use TPP with their example data to calculate a median  EC50 from all the proteins? Actually I want to have the list of proteins which are unaffected, stabilized or destabilized and graph them together,

2) I know in the output (results_TPP_CCR) a column e.g. named "compound_effect_Panobinostat_1" shows which gene is stabilised and which one destabilised but so many blank ones which it does not calculate any pEC50 and other information is missing. So one cannot plot a figure like what they did in Box 3 of their protocol , right? how can i do it?

Many thanks in advance

Hi,

1) This question seems to be related to your other posts

• A: how to plot does response curves using TPP?
• A: how to obtain the curve fitting for all proteins

By default, only those proteins with increasing or decreasing fold changes are considered as affected by the drug and used for curve fitting and pEC50 calculation. The filtering and data transformation prior to dose response curve fitting is explained in detail Box 3 of Franken et al. (2015). Nature Protocols, 10(10), 1567–1593. If you want to increase the number of proteins for curve fitting, it is also possible to relax the filters. To avoid redundancies in this forum, please refer to the answers on the above listed posts for the technical details.

2) The Figures in Box 3 are not produced by default. However, you can create them by plotting the untransformed and transformed fold changes reported in the package output. All relevant values are provided in the wide result table returned by analyzeTPPCCR. For example, the column rel_fc_130H_unmodified_Panobinostat_1 contains the original data for TMT label "130H" in experiment "Panobinostat_1" (blued dots in Box 3 of the paper), whereas rel_fc_130H_transformed_Panobinostat_1 contains the corresponding transformed values (red dots in the same plots). I hope this could answer your question.