Protein Identification by Peptide Mass Fingerprinting

Peptide mass fingerprinting is an effective way of identifying, e.g., gel-separated proteins, by matching experimentally obtained peptide mass data against large databases. However, several factors are known to influence the quality of the resulting matches, such as proteins contaminating the sample in question, modifications altering the mass of the peptides, ionization efficiency of the individual peptides, and the degree of missed cleavage sites. Here, these factors are discussed and methods for elimination of contaminants from the dataset and prediction of various modifications are introduced. Useful tips on how to specify various search parameters and how to manually evaluate the search results are also given.