Continued TPP development influences and is influenced by several other major projects. First, TPP is the primary processing engine behind PeptideAtlas , a resource that reprocesses thousands of publicly accessible datasets, mostly via ProteomeXchange Consortium data repositories, and makes the ensemble results available to the community. PeptideAtlas has reprocessed datasets for dozens of species, and also produces specialized builds for important subtypes of data for certain species, e.g., builds composed entirely of human blood plasma datasets , or phospho-enriched datasets. Raw data files are downloaded from the repositories, converted to mzML, processed with one or more search engines, and validated with the tools described above to carefully control the FDR across all datasets in a build, so that the final combined FDR across all datasets is approximately 1% at the protein level, and much lower at the peptide and PSM levels. PeptideAtlas is made possible by the automatable, high throughput processing of the TPP. The TPP is made more robust by being applied to process public datasets from laboratories from around the world (and fixed or improved when issues are encountered).