Hi Irene,
Unfortunately, that doesn't really tell me much. Exporting the method from Skyline should ensure the transitions match between your WIFF file and Skyline, but for some reason they are not matching.
If you know how in Analyst to show a list of the Q1 and Q3 pairs available in your WIFF file, it would be far more helpful to see that as proof the file contains the right transition m/z values that would be expected to match the targets in Skyline.
If you don't then, I would suggest installing ProteoWizard, if you haven't already, from here:
http://proteowizard.sourceforge.net/downloads.shtml
This might be useful anyway as it will allow you to see your WIFF file as Skyline sees it during import.
Once installed, you can just right-click on your WIFF file in the Windows Explorer and click Open with SeeMS. The SeeMS window that pops up should give you a list of transitions at the bottom.
Sending a screenshot that shows the file contains transition m/z values you expect to match with the ones you have shown in your first screenshot, like:
471.7358, 827.5734
471.7358, 730.4206
471.7358, 616.3777
471.7358, 488.3191
471.7358, 387.2714
476.7579, 837.4816
476.7579, 740.4289
476.7579, 626.3860
476.7579, 498.3274
476.7579, 397.2797
etc.
That would be a good place to start. If it does actually contain these values it will be difficult for me to come up with a reason why they are not matching, but we will get to that once you have shown that it does.
--Brendan