I had a question regarding chromatography. Does it only separate (like in fingerprinting) individual amino acids (that have been cleaved,etc.) or can it also separate "small peptides" as it says in the lecture notes on the web. In the notes, the two terms are used interchangeably, and I was also a bit confused about what you mean by small peptides.
First, paper chromatography DOES separate small peptides (up to, say, 20 AAs). As a peptide gets longer, it tends to precipitate when exposed to the organic solvents used in paper chromatography. Second, fingerprinting does NOT involve paper chromatography or electrophoresis of amino acids. If that were the case, ALL proteins would give the same 20 spots, and it wouldn't be in the least a "fingerprint." Rather, fingerprinting involves the separation of small peptides produced by proteolytic cleavage of a polypeptide at defined sites in the primary structure (e.g., after aromatic (ring-containing) side chains. That way, every different polypeptide yields a different set of small sub-peptides.