This R Markdown document contains a brief introduction to R and R Markdown We explain the capabilities of these tools and their potential implementation together to process Mass Spectrometry data. Then, a simple step-by-step workflow processing of an 8-channel iTRAQ test dataset using the Trans-Proteomic Pipeline and finally a more advanced workflow is described as a template and step-by-step example solution of the 2016 iPRG study as well as an example of how to submit and share such solutions in an R Markdown document.