We presently analyse physiological amino acids in urine, plasma and CSF using the Waters Masstrak Kit on the UPLC.
In nearly all cases for both hydroysate and physiological amino acid analysis following the protocols provided by Waters will be satisfactory. You have left the question very open ended in regards to which AAs in what matrix and at what levels and if performing protein hydrolysis. Most questions are answered on the Amino Acid microsite at http://www.waters.com/waters/nav.htm?cid=514511
Two ways to go:
If analysis is for total amino acids in the fruit (including AAs from protein) you will need to pulp, filter and dilute to get the sugar levels down to less than 0.5% britz. (High level sugars can interfere with the hydrolysis by reacting with amino acids during the hydrolysis procedure)
Then you will hydrolyze sample according to the protocol on the Waters' website under picotag feed analysis.
After hydrolysis an aliquot of the sample can be neutralized with NaOH and analysed according to the normal AccQtag Ultra hydrolysate procedure.
If free amino acid analysis is required you will need to de-proteinize the sample and also get rid of high mw polysaccharides, probably the best way to do this is pulp, dilute with water, filter and the ultra filter a small amount through an ultra filter device similar to the Millipore Ultra free 5,000 cutoff tubes.
If you are using the normal Ultra system and not the MassTrak physiological AA solution be sure to choose the double strength buffer A protocol to ensure separation of asparagine and glutamine from the normal hydrolysate amino acids. This protocol will need careful assessment of results as many other AAs appear in this type of sample and may interfere with your reporting.
I have recently analyzed beer samples with the AccQ.Tag Ultra method. The only sample prep I did before derivatization was a 1:2 dilution of the samples in water. If your samples are cloudy you might need to include a simple filtration (0.45um filter) or centrifugation step.
I have used the Acquity for Amino Acid analysis of proteins and peptides.
You must hydrolize your molecule then derivatize it so that It will be visible using a TUV detector. Does that help?