The Trans-Proteomic Pipeline (TPP) is one of the most widely used, free and open source tool suites for the start-to-finish processing and analysis of shotgun proteomics datasets. It includes tools for format conversion, sequence database and spectral library searching, statistical validation, and protein abundance calculation. BDDS has extended these tools into two pipeline environments, Galaxy and LONI Pipeline. This enables the use of all TPP tools without needing any software to be downloaded and configured. This extension should be of special use to those who are very familiar with proteomics data analysis and workflow environments, but do not have a great deal of experience with TPP itself.