title: "Affinity-proteomics": direct protein identification from biological material using mass spectrometric epitope mapping.
abstract: We describe here a new approach for the identification of affinity-bound proteins by proteolytic generation and mass spectrometric analysis of their antibody bound epitope peptides (epitope excision). The cardiac muscle protein troponin T was chosen as a protein antigen because of its diagnostic importance in myocardial infarct, and its previously characterised epitope structure. Two monoclonal antibodies (IgG1-1B10 and IgG1-11.7) raised against intact human troponin T were found to be completely cross reactive with bovine heart troponin T. A combination of immuno-affinity isolation, partial proteolytic degradation (epitope excision), mass spectrometric peptide mapping, and database analysis was used for the direct identification of Tn T from bovine heart cell lysate. Selective binding of the protein was achieved by addition of bovine heart cell lysate to the Sepharose-immobilised monoclonal antibodies, followed by removal of supernatant material containing unbound protein. While still bound to the affinity matrix the protein was partially degraded thereby generating a set of affinity-bound, overlapping peptide fragments comprising the epitope. Following dissociation from the antibody the epitope peptides were analysed by matrix assisted laser desorption-ionisation (MALDI) and electrospray-ionisation (ESI) mass spectrometry. The peptide masses identified by mass spectrometry were used to perform an automated database search, combined with a search for a common "epitope motif". This procedure resulted in the unequivocal identification of the protein from biological material with only a minimum number of peptide masses, and requiring only limited mass-determination accuracy. The dramatic increase of selectivity for identification of the protein by combining the antigen-antibody specificity with the redundancy of peptide sequences renders this "affinity-proteomics" approach a powerful tool for mass spectrometric identification of proteins from biological material.
authors.affiliation: Department of Chemistry, Analytical Chemistry, University of Konstanz, 78457 Konstanz, Germany.
authors.forename: Marcus
authors.initials: M
authors.lastname: Macht
authors.forename: Andreas
authors.initials: A
authors.lastname: Marquardt
authors.forename: Sören-Oliver
authors.initials: SO
authors.lastname: Deininger
authors.forename: Eugen
authors.initials: E
authors.lastname: Damoc
authors.forename: Markus
authors.initials: M
authors.lastname: Kohlmann
authors.forename: Michael
authors.initials: M
authors.lastname: Przybylski
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000906:Antibodies / Q000276:immunology; D001665:Binding Sites; D018604:Epitope Mapping / Q000379:methods*; D000939:Epitopes / Q000032:analysis* / Q000737:chemistry / Q000276:immunology; D006321:Heart; D066298:In Vitro Techniques; D008969:Molecular Sequence Data; D010455:Peptides / Q000032:analysis / Q000737:chemistry / Q000276:immunology; D011506:Proteins / Q000032:analysis* / Q000737:chemistry* / Q000276:immunology; D040901:Proteomics / Q000379:methods*; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*; D020107:Troponin T / Q000032:analysis / Q000737:chemistry / Q000276:immunology
chemical_list: D000906:Antibodies; D000939:Epitopes; D010455:Peptides; D011506:Proteins; D020107:Troponin T