Finding Protein-Protein Interactions By Mass Spectrometry

Question

[Pappu]

I have a list of several thousand possible interacting partners of a protein obtained from mass spectrometry (SILAC). I am wondering how to filter out possible interacting partners from this list.

What I did so far is to train a HMM from the MSA of known interacting partners in order to search the possible interacting partners in mass spectrometry results. However this would not detect any novel interacting partners if I understood correctly.

Any suggestions will be welcome. Thank you.

[aidan-budd]

Just checking I understand correctly - you'd like to find some way of identifying those proteins proposed as potential interactors that are more likely to be true positives than others?

Also, can I suggest you change the tag from "python" to something like "mass spectroscopy" "protein-protein interactions" etc., I think this might make your post easier for relevant people to identify.

[Pappu]

Exactly I want to find out few potential interacting partners to check experimentally since it is not possible to test all of them.

Answer 1

[aidan-budd]

Caveat - I work in a group where similar questions are worked on, but don't myself do any of it, so these comments aren't from an expert, it's rather based on spending time around experts, so take the ideas with a pinch of salt.

The iELM webserver (developed by Rob Weatherit, who recently left the group I work in) might be useful for you...? You can upload to it a network of interactions, and it will identify potential linear motif-domain interactions within it. These could be candidates for more-likely-to-be-true interactions.

You could also try comparing your network to known networks of interactions - would give you a feeling for how many of the itneractions you see are expected to be seen anyway.

You could compare your list of potential-interactions with lists of known "sticky" proteins - any interactions leading to such proteins are, I guess, less likely to be true interactions than others.

[Pappu]

Thanks for your suggestions. I heard of some groups in Heidelberg doing SILAC. This method is also using HMM based on data from STRING database. So one can actually build a network model of interactions based on the SILAC results. This sounds cool. This reminds me of Bayesian networks. I am wondering if anyone has used it.