Proline a free and open source software suite for mass spectrometry based proteomics.
TPP Institute for Systems Biology "Trans-Proteomic Pipeline"
The categorization of the software and algorithms here is somewhat arbitrary and may change over time. Many programs belong to multiple categories. If you have any suggestions on how to better organize this website - please let us know (see below).
The goal is to continuously improve the website while not moving too far beyond being a classic link collection and repository of free software for data analysis in mass spectrometry-based proteomics and protein analysis. The idea is to maximize the usefulness to anyone facing an analytical or computational problem in proteomics who first would like to know if a solution to the problem already exists and is in the public domain. The list will therefore always be an eclectic mix of full software suites with advanced graphical user interfaces, web-based software, libraries, scripts and pieces of source code to accomplish anything from reading a file in a particular format to providing a complete package for a proteomic analysis pipeline, from sample tracking to storing, viewing and comparing results from protein identification search engines.
The ambition should be to maintain only functional links to tested, useful and gratis software.
IMPORTANT - BY INSTALLING, COPYING OR USING ANY OF THE SOFTWARE YOU (EITHER AN INDIVIDUAL OR A SINGLE ENTITY) AGREE THAT YOU HAVE READ THESE TERMS, UNDERSTAND THEM AND AGREE TO BE LEGALLY BOUND BY THEM. IF YOU DO NOT AGREE TO ALL OF THE TERMS, DO NOT INSTALL, USE OR COPY ANY OF THE SOFTWARE.