A Guide to the Quantitative Proteomic Profiles of the Cancer Cell Line Encyclopedia

We recently reported the quantitative proteomics of 375 samples as part of the Cancer Cell Line Encyclopedia (Nusinow et al., 2020). Mass spectrometry-based proteomics data is broadly unfamiliar to most biologists in our experience, resulting in questions from analysts about how to use the data. From the proteomics community there was interest about how we normalized the data, as the scope of this project was so much larger than what has been commonly available. This paper serves as a guide to the data set to answer these questions and acts as a supplement to the main manuscript. The first part addresses users of the data, describing the experimental design, interpretation of the values, and dealing with standard issues in proteomics like multiple protein isoforms per gene and missing values. The second part of the manuscript details how we arrived at the normalization procedure reported in the paper, including the diagnostics used to assess multiple normalization schemes.