Tackling Misleading Peptide Regulation Fold Changes in Quantitative Proteomics

  • Christoph Gernert
  • Evelin Berger
  • Frank Klawonn
  • Lothar Jänsch
Part of the Advances in Intelligent and Soft Computing book series (AINSC, volume 154)


Relative quantification in proteomics is a common strategy to analyze differences in biological samples and time series experiments. However, the resulting fold changes can give a wrong picture of the peptide amounts contained in the compared samples.

Fold changes hide the actual amounts of peptides. In addition posttranslational modifications can redistribute over multiple peptides, covering the same protein sequence, detected by mass spectrometry.

To circumvent these effects, a method was established to estimate the involved peptide amounts. The estimation of the theoretical peptide amount is based on the behavior of the peptide fold changes, in which lower peptide amounts are more susceptible to quantitative changes in a given sequence segment.

This method was successfully applied to a time-resolved analysis of growth receptor signaling in human prostate cancer cells. The theoretical peptide amounts show that high peptide fold changes can easily be nullified by the effects stated above.


Fold Change Peptide Regulation Human Prostate Cancer Cell Quantitative Proteomics Peptide Group 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Christoph Gernert
    • 1
  • Evelin Berger
    • 1
  • Frank Klawonn
    • 2
  • Lothar Jänsch
    • 1
  1. 1.Helmholtz Centre for Infection ResearchBraunschweigGermany
  2. 2.Ostfalia University of Applied Science, Helmholtz Centre for Infection ResearchWolfenbuttelGermany

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