JMSSJ On-line, Vol. 55 (2007) No. 3, pp. 165-171
Sample Preparation for the Systematic Analysis of a Protein-Protein Interaction Network
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    Shun-ichiro IEMURA and Tohru NATSUME*

    Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), TOKYO, JAPAN

Functional proteomics aims to determine the cellular functions of genes directly at the protein level, and includes the comprehensive analysis of proteinprotein interactions by affnity-based isolation of protein complexes. Mass spectrometry (MS) is a powerful method for the identification of proteins. To enhance the sensitivity and resolution of the MS/MS analysis, we developed a novel direct nanoflow liquid chromatography/MS/MS system. Furthermore, to enhance the sensitivity of the whole analysis system, we optimized the conditions of sample preparation. In this review, we describe the pull-down procedures.

Key words: Proteomics, Proteinprotein interaction, Pull down, Epitope tag, Direct nanoflow LC/MS/MS

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