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bzhanglab / PepQuery

PepQuery: a targeted peptide search engine
http://pepquery.org
GNU General Public License v3.0
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Using PepQuerry for identification of protein-protein interaction #74

Open anuC opened 1 day ago

anuC commented 1 day ago

Hi,

First of all, thank you for such wonderful tool. I'm working with proteins translated from new ORFs and I predicted that the new protein interact with another protein, say for e.g. protein X. Now, I would like to validate this prediction with analysis of available AP-MS datasets for the protein X (bait). Will it be possible to use PepQuery here, to look for whether the new protein present in the interactome of the protein X (using a related approach of 'validating known peptide identification' from PepQuery2 article - Nat. Commu. 2023, 14, 2213).? If so, as a beginner with no prior experience in MS data handling, what are the different steps I should follow after downloading the corresponding thermo raw data?

Any help would be highly appreciated

Thanks in advance Anu

wenbostar commented 1 day ago

The short answer is Yes. Let's move the discussion to email. What is your email?