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Background

Mass spectrometric proteomics

The aims of the group are:

• to develop an interactive, multi-disciplinary approach to protein analytical problems, bringing together scientific expertise from diverse areas such as biology, biochemistry bioinformatics and medicine
• to apply advanced proteome analytical methods based on protein and peptide separation methods, liquid chromatography and mass spectrometry
• to further improve proteome analytical methods including sample preparation to meet the needs in biochemistry and medicine,  to teach students, postdoctoral fellows and practicing scientists in proteomics with a focus on the separation of peptides and proteins and their analysis by mass spectrometry.

The term proteome, which was introduced in 1995 by Mark Wilkins [1], is a hybrid from the words protein and genome, thus implicating the description of the entire protein complement encoded by an organisms DNA. There is a huge difference in complexity between the genome and the proteome, because the genome is more or less static in comparison to the proteome, which is continuously changing from the beginning of life of an individual organism until its death, thereby reflecting the different stages of development as well as the interaction of the organism with its environment. The proteome of an organism is many orders of magnitude larger than its genome. It is estimated that the human genome consists of 20,000 to 25,000 genes [2], which code for much more than 500,000 protein species [3].

Proteomics is a term describing the comprehensive analysis of proteomes. Consequently proteomics focuses on the study of proteins: their chemical structures and their functions, concentrations, localisations, interactions with other biomolecules and their lifetimes.

Mass spectrometry is one of the most important tools for the analysis of the chemical composition of proteins. The analysis of proteins by mass spectrometry became possible by the invention of the "soft" ionization and desorption techniques termed matrix-assisted laser desorption/ionization (MALDI), developed by Karas & Hillenkamp [4] and electrospray-ionization (ESI) by developed by Fenn [5]. The inventions of these soft ionization techniques for the analysis of large biomolecules were rewarded with the Nobel Prize in Chemistry in 2002.

Successful mass spectrometric analysis of proteins critically depends on appropriate sample preparation, which has to ensure that the complexity of the composition of the sample is reduced and that all molecules negatively interfering with the mass spectrometric analysis are removed prior to the analysis of the intact protein or its enzymatic cleavage products. For the reduction of the complexity of a biological sample two main strategies have been established in proteome analysis, the bottom up and the top-down approach (Fig. 1). Bottom-up approach: The proteins are either directly enzymatically digested by an enzyme like trypsin (path 1 in Fig. 1) or separated first by 2-dimensional electrophoresis and then digested gel spot by gel spot (path 2 in Fig. 1). The first approach (path 1 in Fig. 1) requires at least a 2-dimensional separation for reducing the complexity of the peptide mixture. Top-down approach: The proteins of a protein extract are separated firstly and then introduced as intact molecule ions into the mass spectrometer (path 3 in Fig. 1). Liquid chromatography is the most important method applied as the final sample preparation step prior to the mass spectrometric analysis.
 

Figure 1: Main strategies for protein identification in proteomics. A deeper discussion of this figure is given under Research Topics.
1: The shot-gun approach; 2: 2-dimensional electrophoresis approach. 3. Mass spectrometric top-down approach.
2-DE: Two-dimensional electrophoresis. LC: Liquid chromatography. MS: Mass spectrometry. md-S: multi-dimensional separation. PMF: Peptide mass fingerprint. PTM: Posttranslational modifications. ID: identity. -: few information; +: identification of a protein species possible. ++: Comprehensive information allows a more or less full description of the exact chemical composition.

References:
1. Wasinger VC, Cordwell SJ, Cerpa-Poljak A, Yan JX, Gooley AA, Wilkins MR, Duncan MW, Harris R, Williams KL, Humphery-Smith I: Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalium. Electrophoresis 1995, 16(7):1090-1094.
2. She X, Jiang Z, Clark RA, Liu G, Cheng Z, Tuzun E, Church DM, Sutton G, Halpern AL, Eichler EE: Shotgun sequence assembly and recent segmental duplications within the human genome. Nature 2004, 431(7011):927-930.
3. Nielsen ML, Savitski MM, Zubarev RA: Extent of modifications in human proteome samples and their effect on dynamic range of analysis in shotgun proteomics. Mol Cell Proteomics 2006, 5(12):2384-2391.
4. Karas M, Bachman D, Bahr U, Hillenkamp F: Matrix-Assisted Ultraviolet Laser Desorption of Non-Volatile Compounds. Int J Mass Spectrom Ion Proc 1987, 78: 53-68.
5. Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM: Electrospray ionization for mass spectrometry of large biomolecules. Science 1989, 246(4926):64-71.