Perhaps the simplest way to explain is with a couple of screen shots - please see the attached.

Thanks for your interest in Skyline!

Brian Pratt

Thanks a lot!

It proves to be a very useful feature for me!

I noticed that there seems to be 500 Da limit on the size of custom ions, while some of the reporter ions I am looking for are a bit bigger. Would there be a possibility to remove this limitation?

Hi Marek,
You must be using the public v2.6 release. The limit to which you refer was 600 m/z but has been expanded in Skyline-daily to 5000 m/z based on the following feedback:

https://skyline.gs.washington.edu/labkey/announcements/home/support/thread.view?rowId=19327

If you feel it needs to be even greater than 5000 m/z, please explain your need. Otherwise, you can request access to Skyline-daily through the green button on the Skyline download page.

Thanks for your interest in this new feature, and your help in making sure it works for real use.

--Brendan

Dear Brendan,

Thanks for a really quick response. I've just installed Skyline-daily and I see the restriction I'm facing is still there (see attached).

I think this is a different limit than discussed in thread you posted (maximum mass of neutral loss associated with a modification) while I have a large non-peptide backbone ion forming and try to monitor it via special ion (transition settings -> filter -> edit list -> edit... -> (.) custom ion)

Okay. Does 5000 make sense as a limit for this case also?

Thanks for your feedback.

--Brendan

Considering my application 1000 would be enough already. 5000 seems to be a reasonable future-proof limit.
Again, thanks a lot for looking into that!

Marek

Okay. Thanks for the response. The expanded limit will be in the next Skyline-daily release.

--Brendan