Can you send us your Skyline document and your .wiff (or .wiff2) file and the .wiff.scan file that goes with it?

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 also gives you the option to include the .wiff files in the .zip or you could 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

I am not sure I understand which m/z value in the .wiff file is different from what Skyline thinks it should be.
The "method match tolerance m/z" value is what controls how closely the m/z that the mass spectrometer says that it isolated for an MS2 spectrum has to be to the precursor m/z in the Skyline document.
If the observed m/z values in the spectra are shifted, then you would want to adjust one of the "Resolving power" (or "Mass accuracy" if the mass analyzer is "Centroided") values at "Settings > Transition Settings > Full Scan".
-- Nick

Hi Nick,

It worked after I lowered the "Resolving power", thank you so much!

Best wishes,
Mengchun

By the way, the easiest way to see that the resolving power needs to be lowered is to click on a point along the chromatogram.

When you click on a point along the chromatogram, Skyline brings up a spectrum viewer which shows highlighted regions around each transition m/z showing the width of the channel that Skyline summed across in order to extract the intensity at that point.

You can make that channel wider or skinnier by changing the resolution.
-- Nick

Hi Nick,

Is this parameter related to the type of the instrument? I see that the default setting is 30,000 and I lowered it to 5,000, does this mean that the mass spec needs to be calibrated?

Many thanks,
Mengchun