During my final two semesters at Northeastern I have been working with Dr. Olga Vitek and her team to develop the R package MSstats. MSstats is a statistical tool for quantitative mass spectrometry-based proteomics. The package is designed to be used by proteomic researchers so it must be easy to implement without extensive experience in computer science. There are multiple iterations of the package so that many different types of data collection and experimental designs can be modeled.
My main role was to design the publicly available package MSstatsTMTPTM. This package is used to detect differentially abundant proteins and post-translational modifications (PTMs) in experiments with tandem mass tag (TMT) labeling. In order to create the package I needed to include full documentation of my code, including a description of the functions, vignettes, and unit tests.
Additionally, I used the package to create multiple case studies on real world proteomic data. These case studies required me to perform an end to end analysis of the raw data. I transformed the data into the necessary format needed to use the functions of MSstatsTMTPTM, used visualization to effectively summarize the experiments, and modeled the experiments to determine differentially abundant PTMs. Each case study was tailored to the specific research team and their needs. Once the case studies were completed I presented them to the researchers.