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Analytical Chemistry

CRAPome Aggregates Contaminant Info For Protein Interactions

Database helps researchers identify nonspecific binding partners in affinity purification MS experiments

by Celia Henry Arnaud
July 15, 2013 | A version of this story appeared in Volume 91, Issue 28

Affinity purification combined with mass spectrometry is a popular way to determine protein interaction partners. The problem is that the bait proteins used to find interacting proteins can also snag nonspecific partners. Scientists had not found a good way to benefit from the experience of others who have previously caught such contaminants, but a new online database assembled by a large international team of researchers could help. The cleverly named contaminant repository for affinity purification—that’s right, the CRAPome—aggregates data from negative controls for affinity purifications (Nat. Methods 2013, DOI: 10.1038/nmeth.2557). The developers of the repository find that the more abundant a protein is in a given sample, the more likely it is to turn up as a contaminant in interaction studies. Some of the “ubiquitous contaminants,” ones that show up in at least 50% of protein interaction experiments and as many as 90%, include structural proteins such as keratins, tubulins, and actins. But 80% of the contaminants are found in 10% or fewer of the experiments. The repository, which currently includes data for human and yeast proteins, is freely available online at


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