Regarding marine natural product and biotechnology, what is the standard protocol to perform a simple GCMS-based secondary metabolite profiling of an extract of marine animal?
I have never seen anything as better than this one ! A classical guide book-kinda article. A to Z of what you have asked. Attached article (and Link: http://www.nature.com/nprot/journal/v3/n12/full/nprot.2008.182.html).
GC-MS may not be a ideal choice in natural product "discovery" science as far as phytochemistry is considered and when compared to LC-MS or NMR.
I recommend LC-MS analysis for profiling> However, you will find many unknown peaks not identified by the data base of the instrument> You have to isolate these peaks and identify them by NMR techniques