DDA data missing retention time range of specific data file

DDA data missing retention time range of specific data file wangyan2  2024-04-01 12:57

When trying to quantify a set of data (6 total) after DDA using precursor. Skyline miss integrated certain files, which is easy to fix manually, but for one file Skyline won't give me the time window where the peptide eluted. See file attached. While the peptide is detected in all other files at 83 min, for one file the displayed RT window starts at 88 min. How can I fix this?

Nick Shulman responded:  2024-04-01 14:05
If you are extracting MS1 and MS2 chromatograms from DDA data, you should choose "DDA" as the MS/MS Acquisition Method at "Settings > Transition Settings > Full Scan".
If you choose something else such as "DIA" or "PRM" then Skyline will truncate the extracted MS1 chromatograms so that they match the time range over which there were MS2 spectra that matched the precursor.
The reason that Skyline does this is that it's what you would want if you had a scheduled method where you told the mass spectrometer the time range to collect data for your analytes.
The way to tell Skyline not to do this is to choose "DDA" as the acquisition method at "Settings > Transition Settings > Full Scan".

After you change the acquisition method you will need to tell Skyline to extract chromatograms again in order to see a difference. You can do that by using the "Reimport" button at "Edit > Manage Results".

I am not sure whether this is the problem that you are experiencing.
The .sky file that you attached is your Skyline document but it does not include the extracted chromatograms, so I cannot actually see what you are seeing.

If you want to send someone your Skyline document you should use the menu item:
File > Share
which will create a .zip file containing the Skyline document and supporting files including extracted chromatograms.

Files which are less than 50MB can be attached to these support requests. You can always upload larger files here:
-- Nick
wangyan2 responded:  2024-04-02 10:27
Thanks Nick. That resolved my issue.