Evaluation of applicability of tryptic peptide maps for 'finger printing' mitochondrial membrane protein preparations

A background pattern of intense, polar and basic peptides is generated in a mixture of proteins which limits the applicability of “fingerprinting” by peptide maps as a method of establishing homologies among membrane proteins. In addition, it is observed that in such mixtures of proteins the peptide pattern in the “neutral” portion of the map is characterized by a few, weak, tailing peptides which appear on a smeared background of ninhydrin positive material. It is concluded that several types of control maps must be prepared along with maps of membrane fractions if real homologies are to be identified. Application of such control maps to analysis of a sample of mitochondrial membrane protein and a sample of quasicrystalline protein indicated that both of these preparations are disperse mixtures of proteins.