1. If you need to tell Skyline to extract chromatograms again, and you want to preserve all of your manually chosen peak boundaries, you should use the "Reimport" button at "Edit > Manage Results".

2. If you are not seeing the dotted lines for the peak boundaries, you should right-click on the chromatogram graph and select the menu item "Peak Boundaries".

3. If you want to change the Explicit Retention Time of a small molecule, you can right-click on the Molecule in the Targets tree and choose "Modify" and then change Retention Time value in the "Modify Molecule" dialog.
The other way to change the Explicit Retention Time would be to use the Document Grid.
There is a report that you can select called "Small Molecule Transition List" which has a column called "Explicit Retention Time".
You can learn more about custom reports and the Document Grid in the Custom Reports tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

-- Nick

Hi Nick,
Thank you so much!

Regarding my first question: I have a batch with many metabolites that I've already analyzed and manually curated. Now, I’d like to add a new metabolite to my list without losing the information on the metabolites I’ve already analyzed.

If I re-import an Excel file containing my metabolite library with the new metabolite added, Skyline will reprocess the entire list from scratch. How can I preserve the existing analysis while adding the new molecule I want to examine in my samples?

Thanks!

Hi Michal,

Skyline normally would recognize that the transition list is describing things that are already in the document, and only add the new metabolite. If you are seeing something different, it would be great to see your data.

- Brian Pratt