Variability in Streptavidin–Sepharose Matrix Quality Can Significantly Affect Proximity-Dependent Biotinylation (BioID) Data

Due
to their ease of use and high binding affinity, streptavidin-based
purification tools have become widely used for isolating biotinylated
compounds from complex mixtures. We and others routinely use streptavidin–sepharose
matrices to isolate biotinylated polypeptides generated in proximity-dependent
biotinylation approaches, such as BioID or APEX. However, we noted
sporadic, substantial variation in the quality of BioID experiments
performed in the same laboratories over time, using seemingly identical
protocols. Identifying the source of this problem, here, we highlight
considerable variability in streptavidin contamination derived from
different production lots of streptavidin–sepharose beads from
the same manufacturer and demonstrate that high levels of streptavidin
peptide contamination can have detrimental effects on BioID data.
We also describe two simple, rapid approaches to assess the degree
of streptavidin “shedding” from individual lots of the
sepharose matrix before use to avoid the use of lower quality reagent.