Mass error and isobaric peaks analysis

Mass error and isobaric peaks analysis Vahid F  2019-09-06

Hi all,

I have acquired some MS/MS spectra at 120k resolution in PRM mode on QE-HF to be able to resolve small isobaric ions labeled by one 13C or 2H or 15N. Data files are imported into Skyline and I can see the MS/MS in Full Scan panel (picture attached).

The issue is that due to a ~5ppm mass error, m/z that Skyline is looking at is slightly off. Is there a way to force skyline to look at the peaks and not the theoretical m/z or somehow or set a m/z offset? The attached picture illustrates the issue well.


Brendan MacLean responded:  2019-09-07

Hi Vahid,
The setting you are seeking does not currently exist in Skyline. I implemented it once for some poorly calibrated data from a collaborator, but in that case the answer ended up being more complicated than just a single offset, because the mass error varied systematically with the m/z causing curvature when you plotted mass error by m/z: Webinars/Webinar 15/%40files/Webinar 15 (MacLean).pdf#page=25

In the end, the collaborator recalibrated the data outside Skyline and then it worked just file without needing any kind of offset.

I would suggest you pursue a similar solution. There are a lot of tools out there that do interesting things with m/z calibration. Your simple offset request seems like something ProteoWizard msconvert should do, but I am not seeing it in the docmentation:

Maybe check with ProteoWizard support:

Thanks for using Skyline. Sorry, we don't have a great solution for dealing with miscalibration.