Lipoproteins can be separated by these two techniques, one another by molecular size and density, but the fractions obtained are not identical and may not be equivalent análisis.
During ultracentrifugation you will loose apolipoproteins and enzymes which are associated with the lipoproteins. For example in the LDL subclasses LpPLA2 will be found only in the small dense LDL fraction which is an preparative artefact. If you choose other methods you can find LpPLA2 in all LDL fractions.
On the other hand it is nearly impossible to get clear subfractions with FPLC, in the elution fractions you will always find overlapping fractions.
From the perspective of mechanistic systems biology and kinetic modeling, we always want to know what separation technique was used to define lipoprotein fractions. Michael's answer is right on target for ultracentrifugation because protein composition will change in the ultracentrifuge.
A related question that we worry about is: Shouldn't we expect a continuous distribution of lipoprotein size at least for the apoB100-containing lipoproteins? Since LPL and LCAT and PLA2 and CETP and other intravascular processes are constantly modifying lipoprotein composition, we build our models with each lipoprotein species (defined by density or size or apoprotein composition) permitted to have variable lipid composition. The question then becomes: Can we account for the measured compositional and kinetic data given what we know about the intravascular processes AND the characteristics of each subfraction as defined by the separation technology?
I think that there are small differences between the two techniques. FPLC is a softer process, and the integrity, and the recuperation % of the sample is better. In my experience, if study for example the total cholesterol recuperation % by the two techniques (pre and post sample process), FPLC is better. Is for this reason that don´t forget some apolipoproteins, and don´t damage the lipoprotein structure, as occur by ultracentrifugation. In addition, by ultracentrifugation don´t recover all the sample, usually need use a tube slicer or recover the different fractions, while by FPLC recovery all sample because there are not leak. Sometimes is difficult observe the different lipoproteins in the tube, but is use lipid dyes the sample suffer another damage, and by FPLC don´t need eliminate the high salt concentration, required for some test as protein study or some enzymatic determination. Probably this structure damage by ultracentrifugation is due to the high G´s of forces that suffer the sample during separation process, and probably by this reason some apolipoproteins let loose, and finish the process with all albumin at the end of the tube. By FPLC, you can analyze different lipoproteins for determinate the possible mixture, but normally with the cholesterol profile is enough, and can study APOA1 an APOA4, for additional information about HDL or APOB for LDL. This is my opinion after use the two techniques for several years.
Regards.
I do not have experience on separating lipoproteins by FPLC. Nonetheless, I am working on ultracentrifugations for years. It iswell known that some apos are not well determined by ultracenrifugation (as they separated from lipoproteins and recovered together with the botton fraction) although the tecnique permits to separate rasoneable volumes and dilutes less the blood sample diminishing the errors in determining concentrations of lipids and otther lipoprotein compounds. According to my experience, having a well controlled tube slicer (well sharpened, well fixed), leaking is null so no volume losses can be recorded. Of course you have to accurately measure fractions volumes.
Francisco, with amplex you can determinate a lot of parameters infractions separatted by FPLC. Only need an especific oxidase enzime, and the amplex increase the signal. i determinate infractions of FPLC, total cholesterol, free cholesterol, triglicerides, sphingomielin, phosphatidicholine, and apoliproteins by ELISA.