Is "fingerprinting" the first method you discussed in lecture (ie: cleavage of polypeptide with carboxypeptidase)?  Fingerprinting is the process of cleaving a protein with an enzyme that hydrolyzes a polypeptide at limited defined positions within the polypeptide (e.g., the enzyme trypsin cleaves the polypeptide after lysine and arginine residues) followed by 2-dimensional separation of the fragments to produce a series of spots that are characteristic of the protein. Each spot represents a peptide in the range of 5 to 20 amino acids in length. Virtually every different protein will result in a different pattern of spots; the the pattern is called a "protein fingerprint." It does not involve carboxypeptidase, which is used in the sequencing of a polypeptide. The first method discussed in class was the use of carboxypeptidase to produce free amino acids from the C-terminus of a polypeptide. If the free amino acids are isolated sequentially as they are released, then the sequence of the peptide can be determined, if one can identify the amino acids. The methods used to identify the amino acids were paper electrophoresis and paper chromatography. The behavior (migration in paper electrophoresis and/or paper chromatography) of an unknown amino acid can be compared to the behavior of the 20 known amino acids to determine which amino acid corresponds to the unknown.

Fingerprinting is considered a combination of paper electrophoresis and paper chromatography. It takes advantage of both differences in a.a.s' charge and solubilities. So, does a "spot" refer to an amino acid (As would make sense to me) OR to a protein (as I believe was written in one of the answers in the problem set)?
Neither. in fingerprinting the spots are small peptides ("sub-peptides"), fragments derived fromthe original large polypeptide by enzymatic hydrolysis at specific points (e.g. trypsin cleaving after lys and arg). If the spots were singel amino acids, it would be much of a "fingerprint", and nearly all proteins would give the pattern, since nearly all proteins are comprised of all 20 amino acids. p>

For fingerprinting, that gives the amino acid sequence, while paper chromatography only allows one to see whether an amino acid is present?
Fingerprinting itself does not provide the sequence of a polypeptide. It breaks the polypeptide into smaller peptides which are then separated by a combination of paper electrophoresis and paper chromatography. It provides a relatively quick way to identify a protein, since the pattern of spots produced is unique for each protein. Paper chomatography itself can be used to separate amino acids, small peptides, sugars, and many other small organic molecules.

I have a question regarding how paper chromatography impacts a peptide. In problem 2-13 E, I was surprised to see that paper chromatography was the answer. Wouldn't this technique tear the molecules apart, separating the polar amino acids from the non-polar?
In the 1999 exam (problem 2B2), the answer key indicates that fingerprinting does indeed break apart peptides.
Fingerprinting involves several steps. You partially hydrolyze the protein (break it down into short peptides) BEFORE doing the separations. The separations themselves (electrophoresis or chromo.) do NOT break any bonds. They only allow you to separate molecules that have already been broken apart.
(This answer could allow for the electrophoresis half of fingerprinting to be the part of the process which breaks apart the peptide.)

Wouldn't any two fingerprints be identical since both contain (most probably) all twenty amino acids (albeit in different amounts)?  You have the wrong idea about what a fingerprint is. It NEVER involves the
separation of the 20 individual amino acids. Rather it is the separation of fragments of a polypeptide that have been produced by a limited cleavage of the polypeptide. If the proteolytic enzyme trypsin is used, fragments are produced by cleavage after lysine and arginine residues. The fragments are peptide of various sizes (the length being determined by the distribution of arg and lys residues in the polypeptide sequence). Every protein will have a distinctive combination of fragment sizes and compositions.