How can I determine differential ubiquitination of a particular protein using CPTAC proteomics data?

Question

[Alonzo]

I want to check the ubiquitination of a specific protein, divide the samples into high and low ubiquitination levels of that protein, and then test other phenotypic differences between these two groups. The data is from CPTAC, and they have several mzML files as well as the original raw files for each patient sample.

The statistical analysis I can do, but I don't know how to do the proteomics analysis part. First, is this kind of analysis even possible with just this data? If so, can anyone recommend software and a good tutorial for quantifying the levels of ubiquitination on a particular protein for multiple samples and how to somehow get this data into R? Also, can I do this from the mzML files, or will I need the original raw files?

(Sorry if these questions are really basic; I have almost no experience with proteomics.)

Answer 1

[pbpanigrahi]

CPTAC provides the processed data (Protein assembly data and protein relative abundance, PROT files) to users, so you don't have to process mzML files. This file contains abundance values of protein across samples. So its a 2D matrix data where row corresponds to protein and columns to samples. This you can directly import in R after removal of some unwanted columns. Data is normalized log2 ratio of protein abundance, so you don't have to normalize again. However if you do a simple box plot, you will see many noise in the data.

Coming to "ubiquitination of a specific protein", I am guessing you can't do from the processed data, since the processed data contains abundance value of proteins, it does not contain information about the protein whether it is ubiquitinated or not. It does not contain mass information. In that case probably u need to start with MzML files.