ProHits should be used by those users desiring a useful tool to track, annotate and analyze proteomic interaction data. While originally designed to facilitate management and analysis of large scale interacome projects i.e. in the context of a large mass spectrometry facilities, ProHits can still be used for management of more modest projects i.e. in the context of users possessing a single mass spectrometer, or those users that do not have a mass spectrometer at all and simply need a platform for management and analysis of samples submitted to a mass spectrometry core. Whether large or small, we have strived to make the management and analysis tools as easy to use for all types of users via an intuitive user interface.

ProHits was built primarily to help with management and analysis of proteomic interaction data. As such, much of the nomenclature used in the Analyst module and analytical tools e.g. the Cytoscape-Web plugin and SAINT (Significance Analysis of INTeractome) are designed for AP-MS data specifically. This being said, the Analyst module is essentially a relational database that can be used for different types of projects without the need to modify the structure of the database; because the software is released as open source, the end user can modify the code to better suit their needs.

At the moment, we support direct data transfer from X!Tandem, Mascot and SEQUEST search results (note that not all the versions of each search engine are supported; please refer to the user manual for details). Other search engines are supported via the outputs of the Trans Proteomics Pipeline (TPP). Direct support for additional search engines may be added in the future when a clear need has been identified.

We distribute ProHits as a tool to assist in analyzing your mass spectrometry data locally. At the moment, we do not offer any hosting or data analysis services. This said, if you find yourself running into issues that you are unable to resolve, and would like to upload a file for testing, please contact us.

Like all other implementations of ProHits, ProHits Lite VM comes preinstalled with three small demonstration projects that can be explored. We suggest the users familiarize themselves with these projects, as they have been specifically selected to cover the basics of data management and analysis using ProHits and consult the instruction manuals when more in depth instructions are need.

Users wishing to have the ability to securely backup raw files from the mass spectrometer, search these files using parameters tracked by ProHits software, and link the mass spectrometry data to the description of a sample should use the complete version of ProHits. The tracking of the raw mass spectrometry files and search parameters is only possible in the complete version of ProHits: this facilitates data deposition in public repositories, and helps with insuring compliance with reporting standards. The Lite version has been designed for those users who do not desire the entire set of data management applications available through ProHits and wish mainly to use it as an analysis platform. The Lite version enables users to define samples and to link search results to these samples for analysis, but it is up to the user to keep track of the raw file location (and name) and of the search parameters.

The Virtual Machine implementation of ProHits was designed to accommodate users who do not have access to a Linux-based system (i.e. biologists submitting samples to a core facility who only need help analyzing their data). It is not recommend to use the VM implementation as a secure LIMS for a mass spectrometry facility or for large projects. (Sentence on why, data easily lost? Only temporarily stored?) Additionally, the Linux systems (both the complete system and the VM) offer more flexibility and are easier to update as newer versions of the system become available. The ProHits Linux version is easy to install (clear instructions are provided), and an automated updater will be available in future versions.

Funding for ProHits is provided through research grants. The best thing you can do to help us securing future funding is to cite ProHits in your publications (it would be fantastic if you could let us know when you have publications in press). Additionally, you can help by reporting software bugs and by providing suggestions for future improvements and developments. The section "work in progress" is dedicated to tracking user suggestions are our progress in implementing them. Lastly, users that are interested in contributing code for plugins are advised to get in touch.

We ask that you sign up for two reasons: the first reason is so we can send you information regarding major updates to the software (just email us if you want to be removed from this mailing list). The second reason is that by tracking and reporting the number of downloads we are better able to demonstrate to funding organizations the impact ProHits has had on the scientific community, allowing us to increase our chances for securing additional funding.

Initially spectral counts were implemented as a means of quantification because the data is easier to extract, available with any mass spectrometer, and provide a robust way to discriminate between true interaction partners and contaminants in AP-MS data. However, we do realize there are limitations to using spectral count data, and are planning to implement intensity data measures in ProHits in 2013. Stay tuned!

Most of our users perform label-free AP-MS analysis, and as such, we have not received many requests to develop a separate support for SILAC analysis. We are however, supporting the Trans-Proteomics Pipeline (TPP) which comes with two tools for isotopic quantification (XPRESS and ASAPratio). Currently, we are implementing a sorting option based on these ratios within the Analyst module.

Currently, no spectral viewer exists in the analyst module. We are however, working on implementing one. For the time being,spectra can be viewed by opening the page of search results from the original search engine.