How to best use the protein expression data

[seunghun23]

Hi,

I have read the detailed methods on proteomics data processing in the CPTAC papers. However, I am finding it challenging to understand the optimal utilization of the protein expression data provided by the CPTAC package.

While I comprehend that the expression values are relative and centered around zero, I am uncertain about how to use these values for comparative analyses. Here are a few comparisons I am interested in making:

1.Comparing protein expression for a specific gene between a tumor and its matching normal tissue within a particular tumor type.
2.Comparing protein expression for a specific gene across different tumor types.
3.Comparing protein expression for a specific gene across different normal tissues.
4.Comparing protein expression of multiple genes within a single tumor type.

My confusion arises from my uncertainty about whether the normalization was conducted over all cancer types/tissues included in CPTAC or if it was done per disease type. Additionally, I am unclear whether the normalization is per gene or across all genes within a disease type. I would greatly appreciate any clarification or guidance on these points.

Thanks