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.)