Proteom Profiling

What is the impact a mutated protein (e.g. protein involved in signal cascade) on the expression of other proteins / the whole proteome? What are changes in the proteome due to the application of your drug or other compounds? How do visible effects, detectable by differential gene expression (e.g. in Mircoarrays), correlate with differential protein expression? Are you looking for a protein biomarker which correlates for a certain symptom?

These and other questions can be answered precisely with proteome profiling (differential proteome analysis) - the direct comparison of two or more proteomes and thus the identification of differentially regulated proteins, similar to the microarray analysis for transcriptome profiling.

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Mutagenesis Discovery

Genetic mutations (directed/ undirected) are a powerful tool to investigate the corresponding protein function. Does this protein play a crucial role in signal cascades or synthetic pathways? It even may be an approach to elucidate new signal cascades or synthetic pathways.

• • What is the impact of the missing/defect proteins on the proteome?
• • How does the protein network cope with missing/defect interaction partners?
• • What are intracellular targets (e.g. receptors, substrates) of the defect protein?

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Drug Target Discovery

Proteins are targets for diverse pharmaceutical drugs or cosmetic agents. Changes in the proteome are a highly interesting basis for the identification of novel substances.
Alteration in protein pattern due to the application of novel drugs or agents may elucidate also potential side-effects or toxicity.

• • Which proteins are regulated upon the application of new drugs/ agents?
• • Does the new drug/ agent alter the PTM protein pattern and is this part of the

  molecular mechanism?

• • Are there side-effects after drug/ agent application?

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Microarray Follow-up

Analysis of a transcriptome by microarrays or Next Generation Sequencing (NGS) offer a high number of expression data. However, these data provide the overview of gene expression. Corresponding protein expression cannot be analyzed by these techniques. As most cellular changes are due to the regulation by proteins (as receptors, enzymes, structure proteins, hormones) and not by nucleic acids) a proteome analysis is a powerful complementary study.

• • You find interesting changes in the transcriptome?
• • How do these changes correlate with the protein and the PTM pattern?

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Biomarker Discovery

Biomarkers indicate a physiological state of an organism or a certain disease. Proteome studies are a powerful tool for the successful identification of potential protein biomarkers. The proteome of two different states (e.g. healthy group vs. sickened) is being compared for differences in the protein and PTM pattern. Identified biomarker candidates are then verified. Finally, the biomarker has to be transferred to a routine test.

• • Are you looking for a certain protein biomarker?

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