====== Proline Suite ======

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_features.png?400 |}}|
^ Proline suite main features^


The current version support the following features: 
  * **Import identification results** (OMSSA, Mascot and X!Tandem 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).

===== Setup and Install  =====

Read the [[.:setupGuide:start| Installation & Setup documentation]] to install, start the different modules used by Proline or upgrade your installation with a newer version

===== Getting Started =====

Discover [[.:prolineWorkflow| Proline's workflow ]] and how to execute it with Proline Studio and Proline Web.

Discover [[.:msangelWorkflow| MS-Angel ]], a software automating MS/MS identifications and importing these identifications within your Proline projects.
===== How-to =====

Find quick answer to your questions in this [[.:how_to:start]] section.

===== Concepts =====

Read the [[.:prolineConcepts:start|Concepts & Principles documentation]] to understand main concepts and algorithms used in Proline.


===== Raw file conversion to mzDB =====

This procedure is detailed in the [[mzdb_documentation|mzDB Documentation]] section.