I'm looking for proteomic datasets ( LC-MS/MS ) in oncology as a simple matrix of patients/cell lines/ normal vs tumors with spectral counts (any quantified value for protein expression) for each gene. Not from this field. I've been throught https://pdc.cancer.gov/pdc/ the whole day.
I found it's really hard to find and understand the different formats given. A lot of preprocess is necessary from the raw data so I'd like to start for processed spectral counts. ( similar to what we can find with rna-seq)
So any advices from people from this field would be great. Any recent publications with availaible data would be great. For example I took a look to this one Proteogenomic characterization of pancreatic ductal adenocarcinoma but without sucess.
Even the txt files retrieved from deepmap for Quantitative Proteomics of the Cancer Cell Line Encyclopedia are a bit hard to understand.
Will keep diving into it but i'm open to comments.