I would recommend some spectroscopic approaches. I believe IR spectroscopy may be useful, as it helps identifying functional groups, which comes in handy when dealing with oxidized species. I also believe that NMR can be a viable alternative, although data interpretation must be carefully handled.

Thank you for the response. I did tried NMR initially with pure lipids standards and the analysis got increasingly complex as the unsaturation level increased. Also, with a mixture of 2 or more components, it was not possible to assign the signals to the functional groups.

Alpesh, indeed, when you have complex mixtures, especially with lipids, you NMR spectrum can become "chaotic". I would suggest that, whenever possible, you could include two-dimensional NMR analyses (NOESY, COSY, etc.) to help increasing confidence in your results.

If you analysing oxidized phosphatidyl cholines, you can use also specific antibodies recognizing OxPCs described by J. Witztum and collegues. These antibodies are commercially available from Avanti Polar Lipids.

Thank you for the solutions but wanted to ask aren't the antibodies non-specific and were produced using the protein Ox-PL complex of LDL

The antibodies are specific (check the literature): they recognize oxidized PCs but not unoxidized PCs and not óther PL classes. The antibodies recognize both the free OxPCs and protein-bound OxPCs (s. pubmed and annotation to the antibodies E06 on the web site of Avanti Polar Lipids).