No instrument raw file loading ability. This could probably never be fixed unless the instrument vendors port their libraries to OS X. So in short, PEAKS can only read text formats (mgf, mzxml, mzml, pkl, dta, etc) and of course PEAKS projects on OS X.
Images on the summary view is broken. This seems to be a coding issue related to the path (file path on Windows and OS X are different). I do manage to get a workaround though. On the summary view, click "Notes" button on the top of the view, a text editor will show up. Type in the following and click "OK".
<a href="">go</a>A "go" link will be displayed in the "Notes" section of the summary view. Click on the link, the summary view will be correctly displayed in your default web browser.
Vertical tabs are too small and the text on them are not visible. Well, not sure how to workaround this. But when you mouse over the tabs, the tooltips do work.
I will keep playing PEAKS on OS X when I have chance. Please comment if you find other interesting issues :D