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--- how_to:web:quantitationresults [2016/07/06 12:31]
193.48.0.3
+++ how_to:web:quantitationresults [2016/07/06 16:56] (current)
193.48.0.3
@@ Line 23: / Line 23: @@
 {{ :how_to:web:dse_quant_results_proteins_filters.png?nolink |}}
-Double-clicking a Protein will open its summary panel :
+Double-clicking a Protein will open the //Protein details// panel :
+=== Protein details panel ===
 {{ :how_to:web:protein_quanti_details.png?direct |}}
@@ Line 72: / Line 74: @@
 ====== LC-MS Features ======
-This panel lists all the features detected and processed by Proline. By clicking one of them, you can see the corresponding XIC on the right-side panel.
+This panel lists all the features detected and processed by Proline.\\
+Click a **master feature** to see:
+- the corresponding XIC on the right-side panel
+- the corresponding features in each file in the bottom grid (first tab)
+- the corresponding master quant. peptide ion in the bottom gris (second tab).
-{{ :how_to:web:quanti_lcms.png?direct |}}
+You can double click an entry in the bottom grid to open a dedicated tab (feature/peptide ion details).
+{{ :how_to:web:dse_quant_results_features.png?nolink |}}
+----
 ====== LC-MS Peaks ======
 All the peaks are listed here, independently from the features they've been gathered to.
-Click on a Lc-Ms Map name to list all its peaks. By clicking on a peak you can see its XIC charts in the "XIC Viewer" at the bottom of the table, or you can double-click it to open the Xic Viewer in a new tab.
-{{ :how_to:web:quanti_peaks.png?direct |}}
+Click on a LC-MS Map to list all its peaks in the center grid. Note that this grid is provided a filtering tool.
+Click on a peak (center grid) to see its feature and XIC charts in the bottom panel.
+You can alternatively double-click a peak to open the XIC Viewer in a new tab.
+{{ :how_to:web:dse_quant_results_peaks.png?nolink |}}
+----
 ====== Quantitation Stats ======
-**In order to see the ratio values, you have to launch the Profile Analysis from the Summary Panel.**
+==== Post Processing ====
-This tab offers many panel to help you vizualise statistics about your quantitation.
+{{ :how_to:web:dse_launch_post_processing.png?350|}}
+**In order to see the statistics on the ratios, you have to launch the Post Processing (previously called //Profile Analysis//).** Launch it from the //Summary// tab toolbar, or from the quantitation node (in project tree) context menu.
-The first one is a volcano chart of your Proteins based on their -Log10 T-Test P-Value over Log2 Ratio.
+You can see the //Post Processing// configuration window below.\\
+See [[prolineconcepts:lcmsquantitationadvancedconfig| more details on the post-processing parameters]].\\
+Launch the post processing by clicking //Run//. You can watch the task progression in the //Tasks// window. You will also be notified when the task is done. You can then watch the results in the //Quantitation Stats// tab.
+{{ :how_to:web:dse_post_processing.png?nolink |}}
+==== Quantitation Statistics ====
+This tab offers many panel to help you visualize statistics about your quantitation.
+=== Proteins volcano plot ===
+The first panel is a volcano chart of your Proteins based on their -Log10 T-Test P-Value over Log2 Ratio.
+{{ :how_to:web:dse_quant_results_protein_volcano.png?nolink |}}
 The Left grid shows a list of all the proteins, and if they are in the actual boudaries of the selection/exclusion tool.
-The "AC Filters" let you select a color (by clicking on it) and enter an Accession Number (or a part of it) to highlight matching proteins on the chart).
+Hover a dot to see information on the protein.\\
+Click on it to open its [[#Protein details panel|protein details panel]].
+The //AC Filters// let you select a color (by clicking on it) and enter an Accession Number (or a part of it) to highlight matching proteins on the chart). In this example, all proteins containing "HUMAN" in their accession number are colored in orange. By defaults, dots are light blue.
+The //Log2 Fold Change// (of the ratios) and //P-Value// fields let you define new boundaries for the protein selection/exclusion. It's show on the chart with black lines and gray points to show excluded proteins.
-The "Ratio" et "P-Value" let you define new boundaries for the protein selection / exclusion. It's show on the chart with black lines and gray points to show excluded proteins.
+{{ :how_to:web:dse_quant_results_protein_volcano_filtered.png?nolink |}}
-{{ :how_to:web:quanti_volcano_prot.png?direct |}}
+Select a zone with the mouse cursor to zoom on it.
+Use the icon at the top-right of the volcano plot to export it at several picture formats.
-The second tab offers the same volcano chart for peptides, and you can highlight them with a sequence or ptm definition
+=== Peptides volcano plot ===
-{{ :how_to:web:quanti_volcano_pep.png?direct |}}
+The second tab offers the same volcano chart and options for peptides. Instead of accession number, you can color the dots according to their sequence or PTM definition.
+{{ :how_to:web:dse_quant_results_peptide_volcano.png?nolink |}}

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