Dear Lwfhp
Amino acid analysis is not as simple as just hydrolysing the proteins and then analysing it with LC-MS. You will also need to derivatise the amino acids in order to improve both the the separation on a column and/or to aid in visualisation of the amino acid. Have a look at the following book:
http://www.scribd.com/doc/23505508/Amino-Acid-Analysis-Protocols
Two derivatization methods from Waters, Pico-Tag method and the Accu-Tag method, are generally used in the LC-MS analysis of amino acids. Have a look at these links to some of the application notes:
http://www.waters.com/webassets/cms/library/docs/720001946en.pdf
http://www.chromatographyonline.com/lcgc/data/articlestandard//lcgcasia/402006/376668/article.pdf
Also note the amino acid analysis is quite a specialised analytical technique demanding high accuracy and repeatability in sample preparation and analyses, as well as quite expensive derivatisation kits/reagents, standards and columns. If there is any possibility that you can out-source the amino acid analysis of your samples to a facility dedicated to amino acid analysis, I would advise that you do just that. I speak from decades of experience in doing amino acid analyses.
Hope it helps.
Regards
Marina
OK. Things are much clearer now! As Prof. Rautenbach noted, amino acids are fairly difficult to analyze, and generally require advanced skill and experience. Since you are just beginning, it would probably be better to work with systems that are less demanding and then work your way up to more-challenging analyses. First of all, have you had a chance to learn the basics of operating your LC/MS instrument? (Which manufacturer, and which model?)
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