• Sign In
  1. Requests

Ion Match Tolerance MS1 Data Waters Xevo QTOF

support

View Request

view list print
Ion Match Tolerance MS1 Data Waters Xevo QTOF tateh  2025-06-30 11:08
 

Hi,

I'm trying to use MS1 data to do peak quantification in Skyline; however, updating the ion match tolerance does not appear to update the actual range extracted in the chromatogram window. I confirmed with the MassLynx that this ion is present within a range window >0.05 m/z, but when setting the ion match tolerance in Settings > Transition Settings > Library as suggested in this support request: https://skyline.ms/announcements/home/support/thread.view?rowId=31474 , the m/z range for each precursor does not appear to change. The Skyline file was save with the updated ion match tolerance before results were imported.

Thanks in advance!
 
 
Nick Shulman responded:  2025-06-30 12:28
I'm not sure I understand what you are trying to do here.

What sort of data do you have? Is it DDA, PRM, or DIA?

It might be easiest if you sent us your Skyline document and one or more of your waters .raw folders.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

The Share Document dialog gives you the option of including the raw files, or you could zip them up and send them to us separately.
Files which are less than 50MB can be attached to these support requests. You can always upload larger files here:
https://skyline.ms/files.url

The Library Match Tolerance setting that you have highlighted is used when interpreting library spectra, and does not affect chromatogram extraction.

The is a similar looking value "Ion Match Tolerance m/z" on the Instrument tab of Transition Settings. That controls chromatogram extraction in PRM datasets.
For DIA, the matching of MS2 spectra to precursor is done using the isolation scheme that you define on the "Full Scan" tab at Transition Settings.
For DDA, MS2 spectra will match a precursor depending on the Precursor resolution or mass accuracy specified on the Full Scan tab.
-- Nick