Hi Kerry,
There is no command in Skyline for sorting peptides alphabetically in the Targets view, but you can use the Document Grid and then just click the peptide sequence column header to sort (and filter).

I highly recommend having a look at the Custom and Live Reports tutorial:

http://skyline.ms/tutorial_custom_reports.url

With the Document Grid and Live Reports, you can do a lot more than just export reports for use with other software.

You can definitely work with individual transition peak areas either exported or live in the Document Grid. If you install the MSstats tool, it will install its MSstats Input report, which is one example that uses the individual transition peak areas.

Hope this helps. Thanks for posting to the Skyline support board.

--Brendan