An efficient tandem affinity purification procedure for interaction proteomics in mammalian cells

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Abstract
Tandem affinity purification (TAP) is a generic two-step affinity purification protocol that enables the isolation of protein complexes under close-to-physiological conditions for subsequent analysis by mass spectrometry. Although TAP was instrumental in elucidating the yeast cellular machinery, in mammalian cells the method suffers from a low overall yield. We designed several dual-affinity tags optimized for use in mammalian cells and compared the efficiency of each tag to the conventional TAP tag. A tag based on protein G and the streptavidin-binding peptide (GS-TAP) resulted in a tenfold increase in protein-complex yield and improved the specificity of the procedure. This allows purification of protein complexes that were hitherto not amenable to TAP and use of less starting material, leading to higher success rates and enabling systematic interaction proteomics projects. Using the well-characterized Ku70-Ku80 protein complex as an example, we identified both core elements as well as new candidate effectors. *Note: In the version of this article initially published online, the GS-TAP tag in Figure 3b was incorrectly identified as a GC-TAP tag, and the email address for material requests (materials@cemm.oeaw.ac.at) was omitted from the methods section. The errors have been corrected for all versions of the article.