proteoDA: a package for quantitative proteomics

Abstract

proteoDA is an R package designed to analyze high resolution intensity-based mass spectrometry data.proteoDA was designed to be streamlined and user-friendly.proteoDA is built around a DAList, a custom R class, which is used to hold the data, statistical design, and results for a differential abundance analysis.Users import protein abundance data, protein annotation data, and sample metadata into a DAList, and all further functions operate on that list.Once the data are in DAList, proteoDA provides functions for further steps of the analysis Figure 1.