By design the TPP is a collection of separate tools that each specialize in one particular data analysis task. They are all made interoperable via the mzML , pepXML, and protXML formats, where each tool will get its input from one or more of these formats and write its results to one of these formats, except for the conversion tools at the beginning or end of the pipeline. As a collection of individual tools, they are easily amenable to pipelining in a very flexible manner to support a huge variety of combinations and workflows, and a custom program may easily be inserted into the pipeline to support technology development. A summary of the major tools is depicted in Figure .