how_to:studio:xic
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| ====== XIC Quantitation ====== | ====== XIC Quantitation ====== | ||
| + | For description on LCMS Quantitation you can first read the principles in this page : [[prolineconcepts:quantitionprinciple|]] | ||
| ===== Generate a XIC ===== | ===== Generate a XIC ===== | ||
| - | To generate a XIC, right click on the Quantitations Node and select the "Create XIC" menu in the popup. | + | To generate a XIC, right click on the Quantitation Node and select the "Extract Abundances" menu in the popup. |
| {{:how_to:studio:xic_create_popup.png|}} | {{:how_to:studio:xic_create_popup.png|}} | ||
| + | |||
| + | 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 "Clone & Extract Abundances..." menu. | ||
| + | |||
| + | {{:how_to:studio:clonexicpopup.png|}} | ||
| ===== Create Design ===== | ===== Create Design ===== | ||
| To create the Design of your XIC, drag and drop the identifications from the right panel to the left panel. | To create the Design of your XIC, drag and drop the identifications from the right panel to the left panel. | ||
| - | If you drop an identification on the XIC Node, a Group and Sample parents nodes will be automatically created. | + | If you drop an identification on the XIC Node, a Group and Sample parents' nodes will be automatically created. |
| You can also directly drop on a Group or Sample Node. | You can also directly drop on a Group or Sample Node. | ||
| - | {{:how_to:studio:xic_design.png|}} | + | {{ :how_to:studio:xic_quantitation_wizard.png |}} |
| ===== Rename Design ===== | ===== Rename Design ===== | ||
| Line 24: | Line 29: | ||
| * by the right button popup and the menu Rename | * by the right button popup and the menu Rename | ||
| - | We recommand to rename at least the XIC node. | + | We recommend to rename at least the XIC node. |
| - | {{:how_to:studio:xic_rename.png|}} | + | {{ :how_to:studio:rename_design.png |}} |
| ===== Link to Raw Files ===== | ===== Link to Raw Files ===== | ||
| - | To be able to perform a XIC design, we need to know the source raw files. | + | To be able to perform a XIC design, we need to know the source raw files. If any associations between the sample analysis' and the corresponding raw files do not already exist, they can be created at step 2 as shown in the following screenshot. The user just has to drag and drop the correct raw files from the relevant tree to the right. |
| - | + | ||
| - | Proline try to find in the database the corresponding Raw Files already registered. If a Raw file is not found, the icon shows a '!' and you can display the error by expanding the corresponding node. In this case, you will have to select the Raw File by yourself. | + | |
| - | + | ||
| - | Note: To help you, you can display the peaklist tooltip by overriding the Identifcation Node in the Design Tree. | + | |
| - | + | ||
| - | + | ||
| - | {{:how_to:studio:xic_tooltip.png|}} | + | |
| - | + | ||
| - | To select a Raw File, click on the error, and use the following dialog. | + | |
| - | You can select directly a file on the disk or a potential corresponding Raw File registered in the database. | ||
| - | {{:how_to:studio:xic_selectrawfile.png|}} | + | {{ :how_to:studio:raw_files_dialog.png |}} |
| ===== XIC Parameters ===== | ===== XIC Parameters ===== | ||
| When the XIC Design is finished, click on the next button and select the parameters. | When the XIC Design is finished, click on the next button and select the parameters. | ||
| - | See [[prolineconcepts:lcmslabelfreequantitationworkflow|]] to have more details about the different parameters. | + | See [[prolineconcepts:lcmslabelfreequantitationconfig|]] to have more details about the different parameters. |
| - | Note : all the parameters are already set with default values. | + | Note: all the parameters are already set with default values. |
| {{:how_to:studio:xic_create_params.png|}} | {{:how_to:studio:xic_create_params.png|}} | ||
| Line 59: | Line 54: | ||
| You can display its properties, especially the configuration used, by the right mouse button popup: | You can display its properties, especially the configuration used, by the right mouse button popup: | ||
| - | {{:how_to:studio:xic_properties.png?700|}} | + | {{:how_to:studio:xicproperties.png|}} |
| You can delete a XIC Design, see how to [[how_to:studio:delidf|]] | You can delete a XIC Design, see how to [[how_to:studio:delidf|]] | ||
| Line 65: | Line 60: | ||
| You can rename a XIC Design, by clicking on "Rename..." in the popup menu. | You can rename a XIC Design, by clicking on "Rename..." in the popup menu. | ||
| - | You can export the XIC results, see how to [[how_to:studio:exportdata|]] | + | You can export the XIC results, see how to [[how_to:studio:exportdata&#export_an_identification_summary_a_xic_or_a_spectral_count|]] |
how_to/studio/xic.1421143111.txt.gz · Last modified: 2015/01/13 10:58 by 132.168.72.237
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