GC-MS is not a good choice to analyse phospholipid. LC-MS, such as UPLC-ESI-Q-TOF maybe the best. If GC-MS is your only choice, you should perform the derivation fist. Silylation with MSTFA +1% TMCS is often suggested. But be aware that derivation process may cause the degradation and isomery to your compounds. 

How do you propose silylation of cautery fumes done intra-operatively?

I only have access to a GCMS-MS available at my institution. If I want to use anything else, I need to do an inter-institutional collaboration, which increases the amount of waiting and paperwork required.

So that would be your recommendation? I can begin the process of searching for an institution to collaborate with. Thanks. 

Yes. The goal is to obtain a library of phospholipids for neoplastic, pre-neoplastic, and non-neoplastic tissues (the current goal of Royal College of London, I believe) to compare to intra-operatively. Determination of surgical margins would, hopefully, be more precise with this tech.

If you could get access to LC-MS i would recommend using ion pairing reagents they have limits of detection of low ppt (ng L(-1)) for phospholipids. There is a paper in Analyst. 2011 136(8):1586-93. with the title of Use of ion pairing reagents for sensitive detection and separation of phospholipids in the positive ion mode LC-ESI-MS. which goes into great detail and specifics

Thanks, Lillian A. Frink. I looked up the paper, and it seems like it has a lot of information that will prove useful. Thank you.