Bioinformatics Procedures for Analysis of Quantitative Proteomics Experiments Using iTRAQ

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.