• Sign In
  1. Requests

Library MSMS ID line not showing on chromatogram

support

View Request

view list print
Library MSMS ID line not showing on chromatogram laura corveleyn  2023-10-17 03:01
 

Hi,

I made a spectral library in Skyline after manual curation of DIA data from a standard. I exported this library as a blib file and now I want to use this to facilitate annotating the peptides from cell lysates. I loaded it in a new Skyline document and I can see it also includes the retention times, however, I can't see the blue lines showing the MSMS IDs from the library on the chromatogram. I remember I used to right click the chromatogram and click show MSMS ID but I'm unable to find that function. Is this because the library was built using DIA data (and not search results from DDA data)?

Thanks!

Best,

Laura
 
 
Nick Shulman responded:  2023-10-17 07:29
When you right-click on the chromatogram there are a few different things on the "Peptide ID Times" sub-menu ("matching", "from other runs" and "unaligned") which control whether Skyline draws those vertical lines on the chromatogram for psm's where the filename in the spectral library matches the name of the raw file that the chromatogram was extracted from, versus whether it was an unrelated file.

If you send us your Skyline document we could probably tell you what is going on. You can use the "File > Share" menu item to create a .zip file and you can upload it here:
https://skyline.ms/files url
--Nick