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Table of Contents
Vol. 11, No. 1-2, 2006
Issue release date: July 2006
Section title: Research Article
J Mol Microbiol Biotechnol 2006;11:53–81
(DOI:10.1159/000092819)

Mass Spectrometric Identification of Proteins in Complex Post-Genomic Projects

Soluble Proteins of the Metabolically Versatile, Denitrifying ‘Aromatoleum’ Sp. Strain EbN1

Hufnagel P.a, c · Rabus R.b
aBruker Daltonik GmbH, Bremen, Germany, bMax Planck Institute for Marine Microbiology, Bremen, Germany, and cInstitute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany

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Article / Publication Details

First-Page Preview
Abstract of Research Article

Published online: July 10, 2006
Issue release date: July 2006

Number of Print Pages: 29
Number of Figures: 11
Number of Tables: 3

ISSN: 1464-1801 (Print)
eISSN: 1660-2412 (Online)

For additional information: http://www.karger.com/MMB

Abstract

The rapidly developing proteomics technologies help to advance the global understanding of physiological and cellular processes. The lifestyle of a study organism determines the type and complexity of a given proteomic project. The complexity of this study is characterized by a broad collection of pathway-specific subproteomes, reflecting the metabolic versatility as well as the regulatory potential of the aromatic-degrading, denitrifying bacterium ‘Aromatoleum’ sp. strain EbN1. Differences in protein profiles were determined using a gel-based approach. Protein identification was based on a progressive application of MALDI-TOF-MS, MALDI-TOF-MS/MS and LC-ESI-MS/MS. This progression was result-driven and automated by software control. The identification rate was increased by the assembly of a project-specific list of background signals that was used for internal calibration of the MS spectra, and by the combination of two search engines using a dedicated MetaScoring algorithm. In total, intelligent bioinformatics could increase the identification yield from 53 to 70% of the analyzed 5,050 gel spots; a total of 556 different proteins were identified. MS identification was highly reproducible: most proteins were identified more than twice from parallel 2DE gels with an average sequence coverage of >50% and rather restrictive score thresholds (Mascot ≧95, ProFound ≧2.2, MetaScore ≧97). The MS technologies and bioinformatics tools that were implemented and integrated to handle this complex proteomic project are presented. In addition, we describe the basic principles and current developments of the applied technologies and provide an overview over the current state of microbial proteome research.

© 2006 S. Karger AG, Basel


Article / Publication Details

First-Page Preview
Abstract of Research Article

Published online: July 10, 2006
Issue release date: July 2006

Number of Print Pages: 29
Number of Figures: 11
Number of Tables: 3

ISSN: 1464-1801 (Print)
eISSN: 1660-2412 (Online)

For additional information: http://www.karger.com/MMB


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