Proline is a suite of software and components dedicated to mass spectrometry proteomics. Proline lets you extract data from raw files or identification engines, organize and store your data in a relational database, process and analyse this data to finally visualize and extract knowledge from MS based proteomics results.

Proline suite main features

The current version support the following features :

• Import identification results (OMSSA and Mascot files are currently supported). Once imported, search results can then be browsed and visualized through a graphical user interface.
• Validate search results using customizable filters and infer proteins identification based on validated PSM. Identification results issued from the validation can obviously be browsed and visualized.
• Combine individual search results or identification results to build a comprehensive proteome.
• Export identification results in different formats including standard exchange formats.

The software suite is based on three main components:

• A relational database management system storing the data used by the software in four different databases
• A web server handling processing tasks and web data access
• Two different graphical user interfaces, both allowing users to launch tasks and visualize their data: Proline Studio which is a rich client interface and Proline Web the web client interface

An additional component is used by administrators to setup and manage Proline (called ProlineAdmin).

usage scenarios including a Getting started example.

Find quick answer to your questions in this how_to section.

Read the Concepts & Principles documentation to understand main concepts and algorithms used in Proline.

Read the Installation & Setup documentation to install or start the different modules used by Proline.

Both interfaces, Studio and Web, are based on a set of databases.

• MSIdb contains data for a set of identification results. One MSIdb may contains all idenfication results for a given project. See MSIdb Documentation
• LCMSdb. Contains LCMS maps for a given project. See LCMSdb Documentation
• UDSdb contains information on projects, user and identification and/or quantitation experimental plans. See UDSdb Documentation
• PSdb contains information on peptides and ptms seen over all projects (and MSIdb). See PSdb Documentation
• PDIdb contains information on proteins (Accession history, fasta/dat representation, … ). See PDIdb Documentation

This procedure is detailed in the mzDB Documentation section.