There are some numbers that you can specify for peptides in the Document Grid:
Explicit Retention Time
Explicit Retention Time Window

When those numbers have been specified it constrains where Skyline will look for peaks.

If you would like to learn more about the Document Grid (and how to hide/show columns) you can take a look at this tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

Also, if you would like to learn about creating an iRT database with predicted retention times take a look at this tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_irt
--Nick

Hi Nick,

Thanks a lot!

But I figure that by editing the document grid (what I tried is: view -- document grid -- manage reports -- add "explicit RT") you could only manage the way skyline report these data, but not set up the RT window for data processing......?
Could you be more specific about how I could set up the explicit RT window in the software?

Thanks!

After you have specified the Explicit Retention Time and Explicit Retention Time Window, those numbers will be used the next time Skyline needs to pick chromatogram peaks, which happens after Skyline has finished extracting chromatograms.

If you already have some chromatograms in your document, you can tell Skyline to pick peaks again by going to:
Edit > Manage Results > Rescore

If you have set the Explicit Retention Time and Explicit Retention Time Window on a peptide, you should see that Skyline only detects peaks within that window, and that Skyline chooses a peak within that window.

If you have more questions you should send us your Skyline document. In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.
If that .zip file is less than 50MB you can attach it to this support request. You can upload larger files here:
https://skyline.ms/files.url

-- Nick

Hi Nick,

I am sorry, the thing is, I didn't find the place where I could put the values in for the Explicit Retention Time and Explicit Retention Time Window.
I have found a previous skyline support case (https://skyline.ms/announcements/home/support/thread.view?rowId=37483#:~:text=There%20are%20two%20columns%20in,the%20width%20of%20the%20range.&text=But%20Skyline%20will%20look%20within,rather%20than%20lump%20peaks%20together.) where it says to edit these values you should go to "Edit>Insert>TransitionList dialog, called "Explicit Retention Time Window", which I believe is not the case for current skyline versions anymore, since what I found is just blank space without any columns (snapshot attached).

May I know where I could put in the values for the Explicit Retention Time and Explicit Retention Time Window?

If you want to change the set of columns that you see in the Document Grid, you should use "Customize Report" (or sometimes it says "Edit Report") on the "Reports" dropdown.
You should take a look at the Custom Reports tutorial in order to learn how to use the Document Grid:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

"Insert Transition List" is usually only useful for small molecules. There are much easier ways to get peptides into your document, such as "Edit > Insert > Peptides" or "File > Import > FASTA".
After you have peptides in your document, you would use the Document Grid to set the "Explicit Retention Time" and "Explicit Retention Time Window" values on the peptides.
-- Nick

Hi Nick,

Thank you sooooo much! I got it.