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Is anyone aware of a website where they show common false positives often found when doing a TAP-MS experiment to find protein-protein interaction experiments? Particularly the Acs1 protein (Acetyl-CoA synthetase) seems to be a protein I often see in a TAP-MS experiment so I am starting to think it is a false positives but I can't seem to find a good paper or website where it is mentioned as a commonly found false positive interacting protein.

Any insights will be helpful. Thanks.

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The common repository for affinity purification (CRAPome) contains the results from many tandem affinity experiments and scores them based on their presence in control purifications.

The database can be found here. I did a very quick and dirty comparison of the frequency that human ACSL_1 (Uniprot ID; P33121) and GAPDH were detected in control purifications. The graphs shows that ACSL_1 is not a frequent contaminant (detected in less than 5% of GFP control purifications) whereas GAPDH is frequently detected in control affinity purifications.

enter image description here

You can submit your tandem affinity experiments to the CRAPome and it will provide quality scores for your hits. It's very well thought out and not difficult to use. You might want to try it if you're still .

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