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Welcome to ProHits
ProHits is an open source software package (distributed under an Apache 2.0 license) designed to help scientists store, search and analyze mass spectrometry data. Although the platform is flexible and easily amenable to different types of projects, the system is designed to maximize the biological information from high-throughput protein-protein interaction experiments. The platform provides secure storage of mass spectrometry data, integration with search engines and mass spectrometry analytical tools, and web-based queries of the results. An analysis module allows easy visualization of data, comparison of multiple experiments, and permits export to third party software.

We are grateful to multiple members of the open source community who have developed useful software. File conversion is enabled through ProteoWizard. For analysis of Data Dependent Acquisition (DDA) experiments, ProHits currently supports open source search engines Comet, X!Tandem and MSGF+ in addition to continue to provide support for the commercial tool Mascot. Further analysis of the data is provided via the Trans Proteomics Pipeline, notably through PeptideProphet, ProteinProphet and iProphet. For identification and quantification from Data Independent Acquisition (DIA), ProHits now supports DIA-Umpire, MSPLIT-DIA and mapDIA, and enables the creation of assay libraries for the targeted extraction tools OpenSWATH, Skyline and the commercial tool PeakView. In the Analyst module of ProHits, we fully support the statistical scoring tools Significance Analysis of INTeraction (SAINT) and the computationally efficient SAINTexpress. Network visualization is provided through Cytoscape web , and transfer to the prohits-web repository is enabled. Downloaded versions of the data can be further analyzed through the CRAPome interface, or through visualization tools built by our team.

ProHits also tracks all information required for deposition of the data into standards compliant public repositories, as well as for submission of manuscripts to standards compliant journals, and facilitates data export (e.g. to IMEx databases and to ProteomeXchange via MassIVE). The full version of the software is modular and can be readily adapted by programmers to customize data flows. Written in PHP, the main database can be installed on MySQL. Users within a site easily access their results through a web interface, without the need to install additional software. Alternatively, we also distribute a virtual machine implementation of ProHits that can be easily installed on Mac OS X and Microsoft Windows computers.

The project is still under active development, and additional modules and functionality will continue to be integrated in the core database.

ProHits distribution
The source code is available at www.ProHitsMS.com; demo data is included in the downloadable version. Note that an active public site hosted at the Lunenfeld-Tanenbaum Research Institute also contains the same demo data, and is available for navigation via a web interface (without the need for software installation). Because of firewall issues, however, the pages displaying the search results are not available from outside of our Institute.

ProHits team
Core developers:
Guomin (Frank Liu), Jian Ping Zhang, James D.R. Knight

Leadership:
Anne-Claude Gingras

Key collaborators:
Alexey Nesvizhskii’s lab : Chih-Chiang Tsou
Hyungwon Choi
Nuno Bandeira’s lab : Jian Wang
Anne-Claude Gingras’ lab : all lab members
Brian Raught
Mike Tyers
Network Biology Collaborative Centre (Jeff Wrana, co-lead; Karen Colwill, project coordinator)

Funding
• ProHits is currently primarily funded through Ontario Genomics by Genome Canada Genomics Innovation Network node and technology development grants (to J.W. and A.-C.G) and by the Canadian Institutes of Health Research (FDN 143301 to A.-C.G).
• Recent funding for ProHits development, including support for Data Independent Acquisition was provided by the Government of Canada through the joint Genome Canada and CIHR Bioinformatics and Computational Biology LAP program (to A.-C.G., M.T., A.I.N and H.C)
• Additional funding is provided by the National Institutes of Health (to A.I.N and A.C.G., 5R01GM94231; to N.B., 2 P41 GM103484-06A1; to M.T., R01RR024031) and the Singapore Ministry of Education (to H.C., R-608-000-088-112).