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Molecular & Cellular Proteomics 2:1271-1283, 2003.
© 2003 by The American Society for Biochemistry and Molecular Biology, Inc.

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Research

Analysis of Automatically Generated Peptide Mass Fingerprints of Cellular Proteins and Antigens from Helicobacter pylori 26695 Separated by Two-dimensional Electrophoresis^*

Alexander Krah^,,¶, Frank Schmidt, Dörte Becher^||, Monika Schmid, Dirk Albrecht^||, Axel Rack, Knut Büttner^|| and Peter R. Jungblut

From the Core Facility for Protein Analysis and Department of Molecular Biology, Max Planck Institute for Infection Biology, 10117 Berlin, and the ^|| Institute for Microbiology, Ernst Moritz Arndt University Greifswald, 17487 Greifswald, Germany

Helicobacter pylori is a causative agent of severe diseases of the gastric tract ranging from chronic gastritis to gastric cancer. Cellular proteins of H. pylori were separated by high resolution two-dimensional gel electrophoresis. A dataset of 384 spots was automatically picked, digested, spotted, and analyzed by matrix-assisted laser desorption ionization mass spectrometry peptide mass fingerprint in triple replicates. This procedure resulted in 960 evaluable mass spectra. Using a new version of our data analysis software MS-Screener we improved identification and tested reliability of automatically generated data by comparing with manually produced data. Antigenic proteins from H. pylori are candidates for vaccines and diagnostic tests. Previous immunoproteomics studies of our group revealed antigen candidates, and 24 of them were now closely analyzed using the MS-Screener software. Only in three spots minor components were found that may have influenced their antigenicities. These findings affirm the value of immunoproteomics as a hypothesis-free approach. Additionally, the protein species distribution of the known antigen GroEL was investigated, dimers of the protein alkyl hydroperoxide reductase were found, and the fragmentation of -glutamyltranspeptidase was demonstrated.

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