Peptide finger-print

New instrumentation for the analysis of the proteome has been developed including a MALDI hybrid quadrupole time of flight instrument which combines advantages of the mass finger printing and peptide sequencing methods for protein identification (Andersen and Mann 2000). 

Figure 9.15 Typical mass spectrometry based experiment for protein identification/characterization. (1) Proteins are fractionated by chromatography, separated by sodium dodeyl sulphate (SDS) polyacrylamide gel electrophoresis (PAGE), then excised from gel (2) the protein of interest is digested into peptide fragments, that are then (3) identified by ESI MS/MS (4) the first dimension involves molecularion analysis for peptide mass finger-printing (ql, MS only). (5) Tandem MS/MS is used when protein identification is not unambiguous, in which case parent molecular ions are activated by CID (q2) and daughter (product) ions are characterized (ToF) according to the technique of product ion scanning (illustration from Aebersold and Mann, 2003, Fig. 1).

Especially in the fields of amino acids and peptides, such as they are obtained by enzymatic hydrolysis of proteins, a two-dimensional combination of paper or thin-layer chromatography and electrophoresis has become very popular. The patterns of tryptic hydrolysates are termed hnger-prints and can reveal abnormal peptides if mutated anomalous proteins are compared with their normal counterparts. Similar finger-prints can be obtained from nucleic acid digests. 

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