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Improved Two-Dimensional Reversed Phase-Reversed Phase LC-MS/MS Approach for Identification of Peptide-Protein Interactions

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Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
Freie Universität Berlin, 14195 Berlin, Germany
*Tel. +49 30 94793221. Fax +49 30 94793222. E-mail: [email protected]
Cite this: J. Proteome Res. 2012, 11, 2, 1175–1183
Publication Date (Web):November 11, 2011
https://doi.org/10.1021/pr200900s
Copyright © 2011 American Chemical Society

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    Abstract

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    Quantitative mass spectrometry (MS) in combination with affinity purification approaches allows for an unbiased study of protein-protein and peptide-protein interactions. In shotgun approaches that are based on proteolytic digestion of complex protein mixtures followed by two-dimensional liquid-phase chromatography, the separation effort prior to MS analysis is focused on tryptic peptides. Here we developed an improved offline 2-D liquid chromatography-MS/MS approach for the identification and quantification of binding proteins utilizing reversed-phase capillary columns with acidic acetonitrile-containing eluents in both chromatographic dimensions. A specific fractionation scheme was applied in order to obtain samples with evenly distributed peptides and to fully utilize the separation space in the second dimension nanoLC-MS/MS. We report peptide-protein interaction studies to identify phosphorylation-dependent binding partners of the T cell adapter protein ADAP. The results of the SILAC-based pull-down experiments show this approach is well suited for distinguishing phosphorylation-specific interactions from unspecific binding events. The data provide further evidence that phosphorylated Tyr 595 of ADAP may serve as a direct binding site for the SH2 domains of the T cell proteins SLP76 and NCK. From a technical point of view we provide a detailed protocol for an offline 2-D RP-RP LC-MS/MS method that offers a robust and time-saving alternative for quantitative interactome analysis.

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    Lists of identified and quantified proteins of 2-D RP-RP LC-MS/MS experiments. This material is available free of charge via the Internet at http://pubs.acs.org.

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