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We have developed a low-pressure protocol, designed as a rapid, simple and cost-effective procedure for the efficient and parallel purification of multiple peptide mixtures.
As a negative control, we have carried out a parallel purification using lysates from a yeast strain that lack TAP-tagged proteins.
Although neither of these proteins was detected in the negative control (parallel purification from cells expressing the TAP-only vector), it was important to confirm their association with PcG proteins.
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Since phosphorylation/dephosphorylation is known to be important for Feo binding activity we performed two parallel purifications, with and without phosphatase inhibitors (PPI) (Figure 5A).
Neither of these binding partners was detected in parallel purifications from an untagged negative control strain or from several hundred previously studied SPA-tagged bait proteins [13].
Neither of these binding partners were detected in parallel purifications from an untagged negative control strain or from several hundred other TAP-tagged bait proteins [27].
Our sensitivity for peptide detection is typically better than 20 fmol, and the background is usually restricted to trace levels of ribosomal proteins, chaperones and a few other high-abundance common contaminants, as assessed by parallel purifications from untagged E. coli strains.
To ensure that any identified interactions were not mediated through DNA or non-specific interactions with the affinity matrix, we also carried out parallel purifications in which the extract had been pre-treated with nuclease to remove any DNA contamination and from a cell line containing only the empty expression vector.
The purified tight junction fraction appeared specific because a parallel control purification using pre-immune antibodies showed a reasonably clean background (Fig. 4A C).
The synthesis module was expanded with a self-constructed semi-automated formulation unit (Fig. 1) to ensure parallel SPE-purification and formulation of both tracers after HPLC (Fig. 1).
We therefore performed parallel affinity purifications with the StrepTagII and either the 3×FLAG tag or YFP.
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