http://biodev.extra.cea.fr/docs/proline/ 2026-05-06T02:24:14+0200 http://biodev.extra.cea.fr/docs/proline/ http://biodev.extra.cea.fr/docs/proline/lib/tpl/dokuwiki/images/favicon.ico text/html 2016-07-08T08:10:41+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:abbreviations&rev=1467958241&do=diff List of Abbreviations Calc. Mass: Calculated Mass Delta MoZ: Delta Mass to Charge Ratio Ion Parent Int.: Ion Parent Intensity Exp. MoZ: Experimental Mass to Charge Ratio Missed Cl.: Missed Cleavage Next AA: Next Amino-Acid Prev. AA: Previous Amino-Acid text/html 2015-06-30T10:00:36+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:calculator&rev=1435651236&do=diff Calculator Calculator lets you write python scripts to manipulate freely viewed data. 1) To open the calculator, click on the calculator icon (not available on all views for the moment) On the left part of the calculator, you can access to all viewed data, double click to add a table or a column to the script. text/html 2016-05-10T16:23:43+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:changetypicalprot&rev=1462890223&do=diff Chang Typical Protein of Protein Sets :!: The protein sets windows are not updates after a Change Typical Protein ! You should close and reopen the window :!: Open the Dialog To change the Typical Protein of the Protein Sets of an Identification Summary: text/html 2016-07-08T07:50:30+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:connectionmgmt&rev=1467957030&do=diff Connection Management Once user is connected (see startsession), it is possible to : * Reconnect with a different login * Change password text/html 2015-10-28T14:58:28+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:createaggregate&rev=1446040708&do=diff Create a Dataset You can create a Dataset to group your data. To create a Dataset: - right click on Identifications or on an Dataset to display the popup. - click on the menu “Add > Dataset...” On the dialog opened: - fill the name of the Dataset text/html 2015-01-13T15:00:54+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:createproject&rev=1421157654&do=diff Create a New Project To create a Project : - Click on “+“ button at the right of the Project Combobox. The Add Project Dialog is opened. Fill the following fields: - Name : name of your project - Description : description of your project text/html 2015-01-15T10:16:27+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:createuserdisplay&rev=1421313387&do=diff Create a User Window You can lay out your own user window with the desired views. You can do it from an already displayed window, or by using the right click mouse popup on a dataset like in the following example (Use menu “Search Result>New User Window text/html 2016-07-04T11:50:37+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:datamixer&rev=1467625837&do=diff Data Analyzer The purpose of the Data Analyzer is to easily do calculations/comparisons on data. To open the data analyzer, you have two possibilities: - you can use the dedicated button that you can find in the toolbar of all views. If you use this button, the corresponding data is directly sent to the data analyzer. text/html 2016-07-07T10:54:39+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:delidf&rev=1467881679&do=diff Delete Data You can delete Search Results, Identification Summaries and Datasets in the data tree. You can also delete XIC or Spectral Counts in the quantitation tree. The data removal is done at two level and therefore un two operations : * Delete text/html 2016-07-01T17:04:19+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:exportdata&rev=1467385459&do=diff Export Data / Image There are many ways to do an export: - Export a Table using the export button (supported formats: {xlsx, xls, csv}) - Export data using Copy/Paste from the selected rows of a Table to an application like Excel. - Export all data corresponding to an Identification Summary, Xic or SpectralCount text/html 2015-07-10T15:01:37+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:filtertables&rev=1436533297&do=diff Filter Tables You can filter data displayed in the different tables thanks to the filter button at the top right corner of a table. When you have clicked on the filter button, a dialog is opened. In this dialog you can select the columns of the table you want to filter thanks to the text/html 2016-07-01T13:56:53+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:frametoolbars&rev=1467374213&do=diff Frame Toolbars Functionalities A: Display Decoy Data. B: Search in the Table. (using * and ? wild cards) C: Filter data displayed in the Table D: Export data displayed in the Table E: Send to Data Analyzer to compare data from different views F: Create a Graphic : histogram or scatter plot text/html 2016-07-08T08:21:38+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:generatespectrummatches&rev=1467958898&do=diff Generate Spectrum Matches When importing a Search Result in Proline, user can view PSM with their associated Spectrum but by default no annotation is defined. User can generate (and save) this information * For a single PSM, select the icon near the Spectrum (see text/html 2015-07-10T15:03:48+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:histograms&rev=1436533428&do=diff Graphics Create a Graphic There are two ways to obtain a graphic from data: * In the windows with PSM of a Search Result or of an Identification Summary, you can ask for the display of a histogram in a new window to check the quality of your identification. text/html 2015-10-28T15:04:40+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:importmascot&rev=1446041080&do=diff Import a Search Result There are two possibilities to import Search Results: - import multiple Search Results in “All Imported” and put them later in different datasets. - import directly a Search Result in a dataset. Import in "All Imported" text/html 2015-07-10T15:10:36+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:merge&rev=1436533836&do=diff Merge Merge can be done on Search Results or on Identification Summaries. See description for Search Results merging and Identification Summaries merging Merge on Search Results To merge a dataset with multiple Search Results: - Select the parent dataset - Right Click to display the popup - Click on text/html 2016-07-08T08:15:35+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:msdiag&rev=1467958535&do=diff Statistical Reports (MSDiag) In order to launch MSDiag Reports (statistical reports), simply select a node on the tree and choose 'Compute statistical reports' and wait for the results to appear. This applies to a search result only. (not possible for a dataset) text/html 2015-04-09T09:27:25+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:mzscope&rev=1428564445&do=diff Display MzDB Files (with mzScope) From the MzDB tab, you can define your local directory containing the mzDB files by clicking on the button: If you select a file and click on the “View Data” menu in the popup menu, you can display a mzdb file: text/html 2016-07-01T09:29:10+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:newpeaklistsoftware&rev=1467358150&do=diff Update Spectrum using Peaklist software When importing search result, the software used for the peaklist creation has to be specified. This parameter is mandatory or the XIC quantitation as it is used to find scan number or RT in the spectrum title. Indeed, this information is then used to extract abundances in the text/html 2016-09-22T17:09:07+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:preferences&rev=1474556947&do=diff User Preferences The dialog is accessed through the top-bar File submenu. The dialog itself provides the user with the means required to change a series of options according to his personal préférences. For the time being, the number of the available user préférences/settings is minimal. Regardless of the limited for now options, the available user préférences are organized into the following categories. (Subject to change) : text/html 2015-07-10T16:07:03+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:protsetfiltering&rev=1436537223&do=diff How to filter Protein Sets See description of protsetfiltering. :!: The protein sets windows are not updates after filter Protein Sets ! You should close and reopen the window :!: Starting filtering To filter Protein sets of Identification Summaries: - Select one or multiple Identification Summaries to filter text/html 2016-07-04T11:51:29+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:rsproperties&rev=1467625889&do=diff Display Additional Information on Search Result/Identification Summary Functionality Access To display properties of a Search Result/Identification Summary: - right click on a Search Result/Identification Summary - click on the menu “Properties text/html 2016-07-08T08:23:42+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:rsvalidation&rev=1467959022&do=diff How to validate a Search Result See description of Validation Algorithm. Starting Validation To validate a Search Result: - Select one or multiple Search Results to validate - Right Click to display the popup - Click on “Validate...” menu Validation Dialog text/html 2016-02-05T10:10:55+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:searchtables&rev=1454663455&do=diff Search Tables In some tables, a Search Functionality is available thanks to the search button at the top right corner. When you have clicked on the search button, a floating panel is opened. In this panel you can select the column searched and fill in the searched expression, or the value range. text/html 2016-03-24T09:28:57+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:spectralcount&rev=1458808137&do=diff Spectral Count See description of Compare Identification Summaries with Spectral Count . Generate a Spectral Count To obtain a spectral count, right click on a Dataset with merged Identification Summaries and select the “Compare with SC” menu in the popup. This Dataset will be used as reference Dataset and Protein Set list as well as specifics peptides will ne defined there. text/html 2016-07-01T14:49:05+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:startsession&rev=1467377345&do=diff Server Connection When you start Proline Studio for the first time, the Server Connection Dialog is automatically displayed. You must fill the following fields : - Server Host : this information must asked to your IT Administrator. - User : your username (an account must have been previously created by the IT Administrator). text/html 2016-11-10T15:17:27+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:viewprotset&rev=1478787447&do=diff Display MS Queries, PSM, Peptides, Protein Sets, PTM Protein Sites or Adjacency Matrices Functionality Access To display data of an Identification Summary: - right click on an Identification Summary - click on the menu “Display Identification Summary > text/html 2016-07-08T07:52:26+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:viewpsm&rev=1467957146&do=diff Display MS Queries, Peptides/PSM or Proteins of a Search Result Functionality Access To display data of a Search Result: - right click on a Search Result - click on the menu “Display Search Result >” and on the sub-menu “MSQueries” or “ text/html 2015-12-15T10:57:40+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:viewspectralcount&rev=1450173460&do=diff Display a Spectral Count You can display a generated Spectral Count by using the right mouse popup. To have more details about the results, see spectral_count_result The overview is based by default on the weighted spectral count values. (Note: if you sort on the overview column, the sort is based on max(value-mean(values))/mean(values). So, you will obtain the most homogenous and confident rows first) text/html 2015-12-15T10:58:10+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:viewxic&rev=1450173490&do=diff Display a XIC To display a XIC, right click on the selected XIC node in the Quantitation tree, and select “Display Abundances”, and then the level you want to display: Display Protein Sets Protein Sets By clicking on “Display Abundances” text/html 2016-07-01T17:36:05+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:xic&rev=1467387365&do=diff XIC Quantitation For description on LCMS Quantitation you can first read the principles in this page : quantitionprinciple Generate a XIC To generate a XIC, right click on the Quantitation Node and select the “Extract Abundances” menu in the popup. You can also copy an existing Experimental Design and generate a new XIC based on it: select the XIC you want to copy, right click and select text/html 2015-10-28T16:24:47+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=how_to:studio:xicprofilizer&rev=1446045887&do=diff Refine Protein Sets Abundances For description on Advanced Quantitation you can first read the principles in this page : lcmsquantitationadvanced Advanced Protein Sets abundances Right click on the selected XIC node in the Quantitation tree, and select “Refine Proteins Sets Abundances