This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Protein Tool Box is a suite of software modules develop to help the work flow around database search of product-ion spectra. It has modules that prepare the spectra for search, create customized databases, and modules for analysis of database search results. The components are modular and are used in more than one program. It also includes utilities for handling and creation of data to be used by other programs.