The way they used to do it was you purify as much of the protein as you can and then test it with a number of chemical reactions. Their reaction would break off the last amino acid in the chain and then scientists would use the machine to determine which of the 20 amino acids it was. Today they predict the amino acid sequence by sequencing the DNA that encodes the protein.
(http://www.newton.dep.anl.gov/askasci/mole00/mole00255.htm)
(http://www.newton.dep.anl.gov/askasci/mole00/mole00255.htm)
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