annotation question

[Nadia Atallah]

Hello,

At what step do you recommend annotation?  I am assuming that it is best to annotate lipids after quality control, alignment, peak picking, ROI selection etc because then you have fewer to annotate.  And I am planning to use lipid maps next.  I tried using Waters's annotation method,  but I am getting few annotated peaks (and unfortunately none of the statistically significant ones).  I know this is a known issue in lipidomics, but is there some other package/database that works better?  

Any advice would be greatly appreciated.

Thanks,

Nadia