http://biodev.extra.cea.fr/docs/proline/ 2026-05-06T05:12:55+0200 http://biodev.extra.cea.fr/docs/proline/ http://biodev.extra.cea.fr/docs/proline/lib/tpl/dokuwiki/images/favicon.ico text/html 2016-07-05T15:54:49+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:web:createaggregate&rev=1467726889&do=diff Identification Tree and Dataset creation Once your Result Files have been imported, you can use them to create a new Identification Dataset. To create it from result files, you can: * right-click the Identification Trees node in the project tree, then select text/html 2016-07-05T16:58:48+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:web:createproject&rev=1467730728&do=diff Create A Project Open the DataSet Explorer app from the left panel (if it's closed, open it by click on the “apps” button in the upper-left corner of the page) When the DataSet Explorer is opened, you can see your Project Tree on the left. * text/html 2016-07-06T17:13:54+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:web:createquantitation&rev=1467818034&do=diff Create a Quantitation There are 2 ways to open the Quantitation Creation form: * Right-click on the Quantitations node of the project tree, then click New Label Free Quantitation in its menu * Double-click on this node to open the Quantitations table panel. It's empty if you haven't created any quantitation in this project yet. Click the text/html 2016-06-13T13:27:32+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:web:createuser&rev=1465817252&do=diff Create a User You must be logged in as an administrator. Click the gear-shaped button in the top task-bar (circled in blue on the right) to open the administrator settings menu. On the first tab, “User Administration”, you can create a new user by setting up its name, its password, and define whether or not the user will have the text/html 2016-07-04T12:23:18+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:web:delidf&rev=1467627798&do=diff You can delete an Identification dataset by: * right-clicking on it in the project tree and select Move to trash * double-clicking on it to open the Identification panel, then click on Move to Trash in the toolbar of the Summary tab. All deleted datasets are visible in the text/html 2016-07-07T09:36:32+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:web:exportdata&rev=1467876992&do=diff Export Data The “Export” button of any identification or quantitation node is accessible by right-clicking on it, or in its summary tab when you double-click on it. The following window appears: The default name for your output file (e.g. Excel file) is the name of the identification/quantitation. It will also be timestamped to allow multiple exports. text/html 2013-11-26T14:59:24+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:web:importmascot&rev=1385474364&do=diff The first thing to do in your brand new project is to import Result Files. To do so, Click on the “Import Result File” Button, in the toolbar of the project overview window. Note that every button in the sub-windows toolbar are also accessing by right-clicking on the corresponding element in the project tree. If you right-click on your project in the tree, you will see the “Import Result File” button. You should see this window : text/html 2016-07-05T16:53:18+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:web:importresultfiles&rev=1467730398&do=diff Import Result Files The first thing to do in your brand new project is to import Result Files. There are many ways to open the dedicated tab: * Right-click the Imported Search Results node, then click Import result File * Right-click the project node, then click text/html 2016-07-06T16:56:33+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:web:quantitationresults&rev=1467816993&do=diff Double-click on a quantitation node in the Project Tree in order to open its tabbed-panel. Quantitation Summary This panel is a summary of your experimental design, listing your biological groups, their samples and their technical replicates. It also provides the text/html 2014-10-01T15:46:18+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:web:regiserrawfiles&rev=1412171178&do=diff Register Raw & MzDB Files In order to create and run Quantitation analyses, you must register your RAW files and corresponding MzDB files into Proline databses To do so, click on the “Settings” button in the top bar of the Dataset Explorer application, and go to the text/html 2016-07-06T11:21:07+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:web:rsproperties&rev=1467796867&do=diff Display Identification Summary additional informations The Summary panel sums up the validation parameters and results. Summary of an aggregation dataset If you clicked on an Aggregate node, this panel will show the information of the Merged Result Summary and a grid listing all of the identifications of this aggregate. text/html 2016-07-06T17:10:22+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:web:rsvalidation&rev=1467817822&do=diff Validate a Search Result To launch a validation on a dataset: * right-click on its node in the project tree then select Validate tree or * double-click to open identification table, then click Validate tree in the toolbar. The following form appears : text/html 2016-07-05T17:01:56+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:web:startsession&rev=1467730916&do=diff Server Connection Prerequisite : You must have an account to login to the server. Ask your administrator to create one if you don't have any. After the installation, the default account is “admin” with password “admin” - Open your Google Chrome web browser and connect to the adress of the server (ask your administrator) text/html 2016-07-06T11:05:59+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:web:viewprotset&rev=1467795959&do=diff Display proteins sets In order to browse the protein set data of a validated identification, click on the validated identification node in the project tree, on the left side panel of the dataset explorer, and then open the Proteins tab. Proteins grouping text/html 2016-07-06T10:50:01+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:web:viewpsm&rev=1467795001&do=diff Peptides Table The “Peptides” tab of a validated Identification Dataset (or Merged Dataset) allows you to browse the peptides of the related Result Summary. Filters Each table of the Result Summary data viewer provides a set of Filters for Numerical, Text and Boolean data, placed on the left of the grid.