A Case Study on the Comparison of Different Software Tools for Automated Quantification of Peptides

  • Niklaas ColaertEmail author
  • Joël Vandekerckhove
  • Lennart Martens
  • Kris Gevaert
Part of the Methods in Molecular Biology book series (MIMB, volume 753)


MS-driven proteomics has evolved over the past two decades to a high tech and high impact research field. Two distinct factors clearly influenced its expansion: the rapid growth of an arsenal of instrument and proteomic techniques that led to an explosion of high quality data and the development of software tools to analyze and interpret these data which boosted the number of scientific discoveries. In analogy with the benchmarking of new instruments and proteomic techniques, such software tools must be thoroughly tested and analyzed. Recently, new tools were developed for automatic peptide quantification in quantitative proteomic experiments. Here we present a case study where the most recent and frequently used tools are analyzed and compared.

Key words

Automated quantification Mascot Distiller MaxQuant Census MsQuant Rover 



The authors acknowledge the support of research grants from the Fund for Scientific Research – Flanders (Belgium) (project number G.0077.06), the Concerted Research Actions (project BOF07/GOA/012) from the Ghent University, and the Inter University Attraction Poles (IUAP06). We further would like to thank Dr. Bart Ghesquière, Francis Impens, and Evy Timmerman for providing the proteomic data.


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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Niklaas Colaert
    • 1
    • 2
    Email author
  • Joël Vandekerckhove
    • 3
  • Lennart Martens
    • 1
    • 2
  • Kris Gevaert
    • 3
  1. 1.Department of Medical Protein ResearchVIB, Ghent UniversityGhentBelgium
  2. 2.Department of BiochemistryGhent UniversityGhentBelgium
  3. 3.VIB Department of Medical Protein Research and UGent Department of BiochemistryVIB and Ghent UniversityGhentBelgium

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