See Retention Time Recomputing principles if needed.

If you recompute retention time for a given User context, it will not automatically recompute retention time for child contexts (i.e. contexts under the selected context, if exist).
At present, you need to recompute retention time of all your context tree 'manually'. For that, no specific order is needed as final child species are used.

Required conditions to run the Retention Time Recomputing algorithm:

• Selected User context must be grouped
• Protein Grouping on the selected User context must be saved to MSIdb

If above conditions are respected, then follow these steps:

1. Select the User context for which you want to recompute retention time
2. To display the settings dialog:
   • Right-click on the selected context and select Algorithms→Retention Time→Retention Time Recomputing
   • Or, from the main toolbar, select MS Identifications→Context→Algorithms→Retention Time→Retention Time Recomputing
3. Go to the MS Identifications→Context→Algorithms→Retention Time Recomputing to display settings dialog
4. Change algo settings options (see below) if needed and click the Ok button

On top of the dialog, is displayed the User context to process.

Retention Time Alignment panel

• Use alignment coefficients: if you have previously run the Retention Time Alignment algorithm (on the same UserContext you want to recompute RT) and if you want to take into account the alignment coefficients in the retention time computing, check this option

Outliers panel

• Don't take into account outliers: check this option if you want the algorithm to skip final outliers species (based on Grubbs method)

Computing Method panel

• Average: use average to compute the parent species RT from final child species RTs
• Median: use median to compute the parent species RT from final child species RTs
• Weighted average (by score): use average weighted by score to compute the parent species RT from final child species RTs
• Best score per identification + average: from final child species, take for each identification the RT of the best score species then use average to compute the parent species RT
• Best score per identification + median: from final child species, take for each identification the RT of the best score species then use median to compute the parent species RT

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.

Retention times are replaced by new recomputed values for species belonging strictly to the selected User context.
ATTENTION: if other contexts exist below this selected User context, their species retention times are not recomputed.