title: The degradative inventory of the cell: proteomic insights.
abstract: CONCLUSIONS
  Protein degradation has been identified as being deregulated in numerous human diseases. Hence, proteins involved in proteasomal as well as lysosomal degradation are regarded as interesting potential drug targets and are thoroughly investigated in clinical studies.
  
  
  BACKGROUND
  Technical advances in the field of quantitative mass spectrometry (MS)-based proteomics allow for detailed investigations of protein degradation dynamics and identifications of responsible protein-protein interaction networks enabling a systematic analysis of the degradative inventory of the cell and its underlying molecular mechanisms.
  
  
  RESULTS
  In the current review we outline recent technical advances and their limitations in MS-based proteomics and discuss their use for the analysis of protein dynamics involved in degradation processes.
  
  
  CONCLUSIONS
  In the next years the analysis of crosstalk between different posttranslational modifications (PTMs) will be a major focus of MS-based proteomics studies. Increasing evidence highlights the complexity of PTMs with positive and negative feedbacks being discovered. In this regard, the generation of absolute quantitative proteomic data will be essential for theoretical scientists to construct predictive network models that constitute a valuable tool for fast hypothesis testing and for explaining underlying molecular mechanisms.
authors.affiliation: Freiburg Institute for Advanced Studies, School of Life Science-LifeNet, University of Freiburg, Germany.
authors.forename: Rudolf
authors.initials: R
authors.lastname: Engelke
authors.forename: Andrea C
authors.initials: AC
authors.lastname: Becker
authors.forename: Jörn
authors.initials: J
authors.lastname: Dengjel
mesh_terms: D013058:Mass Spectrometry; D040901:Proteomics