The sequence search engine most commonly used with TPP is still Comet , which is actively maintained and advancing with new functionality . A versatile staple among search algorithms and an optimized variation of the original SEQUEST 3 algorithm, it works very well with spectra from any instrument and its scoring algorithm is extremely robust and produces scores that work very well with TPP validation tools. TPP also bundles a slightly customized version of X!Tandem that continues to be a good choice. A newer tool MSFragger is faster in comparison to the current choices of search algorithms included in the TPP, especially when run on large numbers of spectra at one time, due to its fragmentindexing approach. It is not bundled directly in TPP 6.1.0, but is fully supported when installed separately or is available in pre-built TPP containers and images. In future releases, MSFragger will be included within the TPP package.