I am not sure exactly what you are asking.

Can you attach a screenshot of what you are looking at?

By the way, the best way to send someone a Skyline document is to use the:
File > Share
menu item.

This will create a .zip file which will contain all of the necessary files including the .sky and .skyd files that you attached.
The Share Document dialog also allows you to include the raw data files that chromatograms are extracted from.

The .sky and .skyd files that you attached do not exactly go with each other, so I am not exactly sure how things looked for you.

One way to deal with two molecules which have different predicted retention times is to tell Skyline that they each have a different "Explicit Retention Time". You can right-click on a molecule in the Targets tree and choose "Modify" and then provide a value for "Retention time" in the "Explicit values (optional)" section of the Modify Molecule dialog.
This works well if your run-to-run retention times are consistent enough.
-- Nick

Hi Nick,
Thanks for your suggestions.

I did add the explicit retention time for isomers (isobutyrate and butyrate) but did not show peak areas for their respective CEs. Although, without adding that parameter Skyline did pretty good by selecting the high abundance peaks for the acetate, lactate, propionate.

Please look into attached files and suggest if I am doing something wrong in selecting peaks.

Thanks,
Ujjal

Unfortunately, if your Skyline document contains multiple molecules with the same precursor m/z, you cannot do CE optimization.
The workaround is to create separate Skyline documents so that no document has duplicate precursor m/z's.
This needs to be done before you export the method, because if you export a CE optimizing method where multiple precursors have the same m/z, Skyline will not be able to make sense of the results when it tries to import them.

We first discovered this limitation in 2016, and decided at the time that we were not going to fix it.
I cannot remember exactly how we came to that conclusion but I think it seemed that it was going to be very difficult to fix.

In theory, it might be possible for us to fix this now. Skyline is able to read a lot more information from the raw files, including the actual collision energy values, so Skyline does not really need to be doing the thing it does right now which is to vary the Q3 values in the exported method by 0.01 in order to indicate which step of the collision energy they are for.
Also, it probably would have been nice if Skyline had warned you about the duplicate precursor m/z's when you exported your method.

-- Nick

Thanks Nick for your support.