The answer would be broken into three parts:

*best chromatographic condition

*best ionization condition

*best instrument condition for ion mobility separation

Are these phospholipids, neutral lipids, or otherwise?

For phospholipids, for example, I prefer normal phase to reverse phase separation (however, normal phase takes significantly more equilabration time than reverse phase but speration is genrally better if going for the maximum number of polar lipid classes). I prefer profiling in negative ion electrospray, as fatty acids come off as carboxylate anions in MS/MS. Other other hand, positive ion electrospray is better for head group identification. However, once method is understood, lipids are associated with retention time and negative ion work can do quite well, and give comprehensive acyl chain profile.

For neutral lipids I prefer reverse-phase separation. Total lipid extracts can be taken and separated further by aminopropyl SPE, and the neutral fractions analyzed in positive ion electrospray with ammonium ion adduction. Lithium also works.

For fragmentation in Synapt, I suppose it will depend on whether you will be using the IMS plot as a method of analysis versus just analyzing the MS/MS spectra.

Hi, we recently published a method for lipidomic analysis on a UPLC/qTOF system (SynaptG1). You can find it on RG (Knittelfelder et al.).