• Sign In
  1. Requests

Isolation offset PRM Astral

support

View Request

view list print
Isolation offset PRM Astral johannes fuchs13381  2025-11-19 02:41
 

Hi,

I have a question using a targeted-MS2 method from an Astral mass spectrometer. I would like to set an isolation offset to shift the quite narrow isolation with of the Astral to get a second isotope into the isolation window, without increasing the isolation width.

In Transition Settings - Full Scan - MS/MS filtering I can set PRM, but this will exclude most of the peptides, as the precursor mass in the tMS2 scans get a different precursor mass. If I try a workaround and set the scan filter to DIA, skyline ignores the peptides selected from the library, and tries to match ions to all possible peptides in the library.

Is there a way to use isolation offset in PRM experiments?

Thanks for any help!

Johannes
 
 
Nick Shulman responded:  2025-11-19 09:37
There is no straightforward way to get this work with Skyline. There are convoluted ways to get it to work involving converting to .mzML and doing search and replace on the mzML text file to trick Skyline into thinking that spectra isolated the precursor m/z that Skyline was expecting. There also might be a way to get this to work using the relatively new "spectrum filter" feature:
https://skyline.ms/home/software/Skyline/wiki-page.view?name=SpectrumFilters

In general, people always want to only fragment the monoisotopic m/z for MS2 chromatograms. The reason for this is that the monoisotopic mass only produces monoisotopic fragments, whereas the M+1 mass produces a mixture of monoisotopic and M+1 fragments. Therefore, even in cases where the M+1 peak is larger than the monoisotopic peak, you still get better MS2 signal when you only fragment the monoisotopic precursor.

A couple of years ago someone asked a similar question about wanting to select the entire precursor isotope envelope for fragmentation:
https://skyline.ms/announcements/home/support/thread.view?rowId=37846

So far, we have not seen a scenario where isolating anything other than the monoisotopic peak improved things, which is the main reason this is not supported in Skyline.
-- Nick