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| ====== Proline Suite ====== | ====== Proline Suite ====== | ||
| - | Proline is a suite of software and components dedicated to mass spectrometry proteomics. Proline lets you organize your data, process and analyse them to finally 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. |
| - | {{ :proline_features.png?300 |}} | + | |
| - | The current version support the following features : | + | |{{ :proline_features.png?400 |}}| |
| - | * 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. | + | ^ Proline suite main features^ |
| - | * 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. | + | |
| - | * Merge individual search results or identification results to build a comprehensive proteome. | + | |
| - | * 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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