We have described the many components of the latest version 6.1.0 of TPP, which has been under continual development since its original tools were published in 2002. Although several TPP tools have been re-written to be faster and superior to the previous versions, and nearly all tools have been extended and optimized since their original release and subsequent publication, the core capabilities are everpresent and overlayed with modern processing tools to deal with new workflow demands. Development in the TPP ecosystem will continue in the future, with further extension of existing tools as well as the addition of new tools as demanded by users. Special areas of focus include the enhancement of quantitation tools to keep up with evolving quantitative techniques, as well as bundling and development of post-quantitation tools such as batch-effect correction, imputation, clustering, and visualization. We will also extend the DISCO workflow to merge the library-free and library-based analyses to leverage the best of both approaches.