protein identification by peptide mass fingerprinting
is an analytical technique for identifying unknown protein. Proteins to be identified is first digested into peptides, whose absolute mass can be accurately analyzed by a mass spectrometer, such as MALDI-TOF or ESI-TOF. MALDI is more preferred in PMF analysis, as it has a wide sequence coverage and can analyze a large amount of sample at the same time. The peptide mass are compared to database containing the theoretical peptide masses of all known protein sequences. The match with the highest score was considered to be the identity of the unknown protein. As only the masses of peptide, not the exact sequence of peptides, are measured, there can some interference to the mass match. For example, post-translational modification results in up-shift of the peptide mass, and contamination of other protein also affect the accuracy of the analysis. Therefore, large portion of post-translational modifications and high contamination of other proteins should be eliminated before the analysis. Creative Proteomics provides Peptide Mass Fingerprinting (PMF) analysis and ions searching against database for rapid identification of proteins.