Mass spectrometry has quickly become an essential tool in molecular biology laboratories. Here, we describe the Trans-Proteomic Pipeline, a collection of software tools, to facilitate the analysis, exchange, and comparison of MS data. The pipeline is instrument-independent and supports most commonly used proteomics workflows, including quantitative applications such as ICAT, iTRAQ, and SILAC. Importantly, the pipeline uses open, standard data formats and calculates accurate estimates of sensitivity and error rates, thus allowing for meaningful data exchange. In this chapter, we will introduce the various components of the pipeline in the context of three typical proteomic use-case scenarios.