Did somebody compare filtration (for instance with Millipore centrifugal filters) versus precipitation (for instance with acetonitrile) for the analysis of amino acids in cell culture supernatants?

If yes, do you use internal standars?

There has been a chain on something like that. We have done comparisons a few times, though probably only one with an amino acid (synthetic, relatively hydrophobic). Generally: You can get rid of proteins with ultra-filters more conveiently than with precipitation (usually more extensively also).
With ultra-filtration you need to whatch that your analyte does not adhere to the proteins. Denaturing the proteins helps, but more important is to add something (alcohol...) which increases the solubility of your analyte in the liquid part.