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| ====== Proline Suite ====== | ====== Proline Suite ====== | ||
| - | Proline is a suite of software and components dedicated to mass spectrometry proteomics experiments processing and analysis. Proline lets you organize, visualize and extract knowledge from MS based proteomics results : | + | 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. |
| - | * Import identification results (OMSSA and Mascot result 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. | + | |{{ :proline_features.png?400 |}}| |
| - | * Merge individual search results or identification results to build a comprehensive proteome. | + | ^ Proline suite main features^ |
| - | * Export identification results in different formats including standard exchange formats. | + | |
| + | |||
| + | 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: | 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 **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 | + | * 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: | + | * 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 |
| - | * ProlineStudio which is a rich client interface | + | |
| - | * ProlineWeb the web client interface | + | |
| An additional component is used by administrators to setup and manage Proline (called ProlineAdmin). | An additional component is used by administrators to setup and manage Proline (called ProlineAdmin). | ||
| - | ===== Use Cases ===== | + | ===== Setup and Install ===== |
| - | usage scenarios including a **Getting started** example. | + | 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 ===== | ===== How-to ===== | ||
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| Read the [[.:prolineConcepts:start|Concepts & Principles documentation]] to understand main concepts and algorithms used in Proline. | Read the [[.:prolineConcepts:start|Concepts & Principles documentation]] to understand main concepts and algorithms used in Proline. | ||
| - | |||
| - | ===== Setup and Install ===== | ||
| - | |||
| - | Read the [[.:setupGuide:start| Installation & Setup documentation]] to install or start the different modules used by Proline. | ||
| - | |||
| - | ===== Releases ===== | ||
| - | |||
| - | Both interfaces, Studio and Web, are based on a set of databases. | ||
| - | |||
| - | |||
| - | ===== Database Models ===== | ||
| - | |||
| - | * MSIdb contains data for a set of identification results. One MSIdb may contains all idenfication results for a given project. See [[MSIdb_documentation| MSIdb Documentation]] | ||
| - | * LCMSdb. Contains LCMS maps for a given project. See [[LCMSdb_documentation| LCMSdb Documentation]] | ||
| - | * UDSdb contains information on projects, user and identification and/or quantitation experimental plans. See [[UDSdb_documentation| UDSdb Documentation]] | ||
| - | * PSdb contains information on peptides and ptms seen over all projects (and MSIdb). See [[PSdb_documentation| PSdb Documentation]] | ||
| - | * PDIdb contains information on proteins (Accession history, fasta/dat representation, ... ). See [[PDIdb_documentation| PDIdb Documentation]] | ||
| ===== Raw file conversion to mzDB ===== | ===== Raw file conversion to mzDB ===== | ||
| This procedure is detailed in the [[mzdb_documentation|mzDB Documentation]] section. | This procedure is detailed in the [[mzdb_documentation|mzDB Documentation]] section. | ||
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