Peptide mass fingerprinting
Peptide mass fingerprinting (PMF), also known as protein fingerprinting, is an analytical technique for
The advantage of this method is that only the masses of the peptides have to be known. A disadvantage is that the protein sequence has to be present in the database of interest. Additionally most PMF algorithms assume that the peptides come from a single protein.
Origins
Due to the long, tedious process of analyzing proteins, peptide mass fingerprinting was developed. Edman degradation was used in protein analysis, and it required almost an hour to analyze one amino acid residue.[9] SDS-PAGE was also used to separate proteins in very complex mixtures, which also employed methods of electroblotting and staining.[10] Then, bands would be extracted from the gel and sequenced, automatically. A recurring problem in the process was that interfering proteins would also purify with the protein of interest. The sequences of these interfering proteins were compiled into what came to known as the Dayhoff database.[11] Ultimately, having the sequences of these known protein contaminants in databases decreased instrument time and expenses involved in protein analysis.
Sample preparation
Protein samples can be derived from
Then the proteins are cut into several fragments using proteolytic enzymes such as trypsin, chymotrypsin or Glu-C. A typical sample:protease ratio is 50:1. The proteolysis is typically carried out overnight and the resulting peptides are extracted with acetonitrile and dried under vacuum. The peptides are then dissolved in a small amount of distilled water or further concentrated and purified and are ready for mass spectrometric analysis.
Mass spectrometric analysis
The digested protein can be analyzed with different types of mass spectrometers such as ESI-TOF or
A small fraction of the peptide (usually 1 microliter or less) is
Coupling ESI with capillary LC can separate peptides from protein digests, while obtaining their molecular masses at the same time.[15] Capillary electrophoresis coupled with ESI-MS is another technique; however, it works best when analyzing small amounts of proteins.[13]
Computational analysis
The mass spectrometric analysis produces a list of molecular weights which is often called a peak list. The peptide masses are compared to protein databases such as