how_to:alignretentiontime
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| ====== How to align retention time ====== | ====== How to align retention time ====== | ||
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| + | See [[userguide:retentiontimealignment|Retention Time Alignment principles]] if needed. | ||
| ===== Run the Retention Time Alignment algorithm ===== | ===== Run the Retention Time Alignment algorithm ===== | ||
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| {{ :how_to:rtalignmentmenu.png |Retention Time Alignment menu}} | {{ :how_to:rtalignmentmenu.png |Retention Time Alignment menu}} | ||
| - | - Select the User context you want to align | + | :!: **Required condition to run the Retention Time Alignment algorithm:** |
| - | - Go to the ''MS Identifications->Context->Algorithms->Retention Time Alignment'' to display settings dialog | + | |
| + | * **Selected User context must be grouped** | ||
| + | |||
| + | If above condition is respected, then follow these steps: | ||
| + | |||
| + | - Select the User context you want to align (You first need to [[how_to:proteingrouping|group proteins]] for this context and [[how_to:savetomsidb|save]] it) | ||
| + | - To display the settings dialog: | ||
| + | * Right-click on the selected context and select ''Algorithms->Retention Time->Retention Time Alignment'' | ||
| + | * Or, from the main toolbar, select ''MS Identifications->Context->Algorithms->Retention Time->Retention Time Alignment'' | ||
| - Change algo settings options (see below) if needed and click the ''Ok'' button | - Change algo settings options (see below) if needed and click the ''Ok'' button | ||
| {{ :how_to:rtalignmentgui.png|Retention Time Alignment settings}} | {{ :how_to:rtalignmentgui.png|Retention Time Alignment settings}} | ||
| - | ==== Algo settings options ==== | + | ==== Algo settings options (The default options are generally optimal) ==== |
| On top of the dialog, are displayed the following information: | On top of the dialog, are displayed the following information: | ||
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| **Performance panel** | **Performance panel** | ||
| * ''Use memory tuning'': if NOT selected, the process will be faster but memory consuming. If selected, the process will be a little bit slower but memory efficient. | * ''Use memory tuning'': if NOT selected, the process will be faster but memory consuming. If selected, the process will be a little bit slower but memory efficient. | ||
| - | |||
| {{:how_to:rtalignmentendmessage.png |}} | {{:how_to:rtalignmentendmessage.png |}} | ||
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| Each aligned identification has two new [[how_to:accessidentificationinfos|properties]]): | Each aligned identification has two new [[how_to:accessidentificationinfos|properties]]): | ||
| - | * ''a'': slope of the linear regression | + | * ''slope'': slope of the linear regression |
| - | * ''b'': intercept of the linear regression | + | * ''intercept'': intercept of the linear regression |
| - | * ''reference'': reference user context (not yet available) | + | * ''reference'': reference user context |
| {{:how_to:rtalignmentidfproperties.png|}} | {{:how_to:rtalignmentidfproperties.png|}} | ||
| + | |||
| + | |||
| + | :!: You can access your identification properties either from identifications under your user context, or the under the appropriate search contexts. If you look at the identification properties just after running the Retention Time Alignment algorithm, it may not refresh immediatly. | ||
| ===== Apply alignment results ===== | ===== Apply alignment results ===== | ||
| - | See Recompute Retention Time algorithm. | + | To apply alignment coefficients on species, you need to [[how_to:recomputeretentiontime|Recompute Retention Time]]. |
| + | |||
| + | :!: **ATTENTION** \\ | ||
| + | During alignment process, retention time are predicted using an external utility and stored in peptide properties (peptides belonging to the reference context). These values are NOT the final recomputed retention times, they are only used by the retention time alignment algorithm.\\ | ||
| + | {{:how_to:rtalignmentpredproperty.png|}} | ||
how_to/alignretentiontime.1279544812.txt.gz · Last modified: 2010/07/19 15:06 by 132.168.74.230
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