Commentary

The speciation of the proteome

Peter R Jungblut¹ , Hermann G Holzhütter³ , Rolf Apweiler² and Hartmut Schlüter³

¹  Max Planck Institute for Infection Biology, Core Facility Protein Analysis, Berlin, Germany

²  European Bioinformatics Institute, Cambridge CB10 1SD, UK

³  Charité Berlin, Institut für Biochemie, Berlin, Germany

author email corresponding author email

Chemistry Central Journal 2008, 2:16doi:10.1186/1752-153X-2-16

Published:	18 July 2008

Abstract

Introduction

In proteomics a paradox situation developed in the last years. At one side it is basic knowledge that proteins are post-translationally modified and occur in different isoforms. At the other side the protein expression concept disclaims post-translational modifications by connecting protein names directly with function.

Discussion

Optimal proteome coverage is today reached by bottom-up liquid chromatography/mass spectrometry. But quantification at the peptide level in shotgun or bottom-up approaches by liquid chromatography and mass spectrometry is completely ignoring that a special peptide may exist in an unmodified form and in several-fold modified forms. The acceptance of the protein species concept is a basic prerequisite for meaningful quantitative analyses in functional proteomics. In discovery approaches only top-down analyses, separating the protein species before digestion, identification and quantification by two-dimensional gel electrophoresis or protein liquid chromatography, allow the correlation between changes of a biological situation and function.

Conclusion

To obtain biological relevant information kinetics and systems biology have to be performed at the protein species level, which is the major challenge in proteomics today.