Bioinformatics Procedures for Analysis of Quantitative Proteomics Experiments Using iTRAQ

  • Pim van NieropEmail author
  • Maarten Loos
Part of the Neuromethods book series (NM, volume 57)


The combined use of liquid chromatography followed by tandem mass spectrometry (LC-MS-MS) in proteomics research has proven to be a valuable asset in the success of this field of science. Advances in LC-MS-MS technology have allowed researchers to identify an increasing number of proteins from complex biological preparations in a high-throughput fashion. Moreover, techniques based on the labeling of peptides with stable isotopes have made it possible to determine relative differences in abundance of proteins between biological samples. As has been the case for microarray technology, the newly emerging field of quantitative proteomics is associated with the development of novel bioinformatics and statistical approaches that, within the boundaries of particular aspects and limitations of the technique, allow us to ask biological questions and derive meaningful answers (1–3). In this chapter, we describe a protocol of an integrated bioinformatics workflow that deals with the identification of proteins and the relative quantification using iTRAQ labeling in complex proteomics experiments that also involves comparison of quantitative data obtained in separate LC-MS-MS runs.

Key words

Proteomics iTRAQ Bioinformatics Protocol Mascot server Sequence clustering 



The authors would like to thank Roel van der Schors for his assistance and Matrix Science for correction of the manuscript.


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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive ResearchVU UniversityAmsterdamThe Netherlands

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