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ProHits is a laboratory information management system that allows for the storage and analysis of MS data with a focus on interaction proteomics.

Mass spectrometry data can be a challenge to manage, appropriately and efficiently analyze, and subsequently present to an audience in simple and intuitive ways. Data needs to be archived, searched, scored, compared and visualized, often requiring a variety of tools. For interaction proteomics, keeping track of the cell line, bait and experimental conditions is also of paramount importance. ProHits was specifically designed to handle many of these challenges, and our 2012 protocol protocol provides much of the details regarding the use of the software, notably in scoring interaction proteomics data and for running ProHits as a virtual machine implementation.

Recent additions to this release of ProHits (v.4.0) include the incorporation of tools for the handling of Data Independent Acquisition samples, including the comprehensive computational framework DIA-Umpire, the spectral searching tool MSPLIT-DIA and the statistical quantification tool mapDIA. A module dedicated to interaction proteomics enables interrogation and scoring of DDA or DIA data via Significance Analysis of INTeractome (SAINT) software, including SAINTexpress, and transfer to a public quantitative interaction repository, ProHits-web. We have recently coupled data scoring with visualization tools that are capable of displaying multiple parameters from quantitative protein–protein interaction data sets in a variety of ways. Lastly, ProHits now facilitates deposition of the data in ProteomeXchange, through MassIVE. The open source system ProHits now handles and/or facilitates the storage, searching, interrogation, analysis and visualization of both DDA and DIA MS data, functioning as a single easy to use post-acquisition pipeline.

Watch a series of short instructional videos.
MS Data Management module
Analyst module

Install either the full ProHIts system or the ProHits Virtual machine

Read installation and user manuals.