So...you set up this elegant phosphoproteomics project. You dual step enriched, you used a brilliant LC-MS method with neutral loss triggered ETD and now you have this fantastic list of 163 phosphorylation sites that are up-regulated by your drug. What the heck do you do with it now?
Well...you can convert it to gene identifiers if you are in mouse or human and give it to Ingenuity Pathways Analysis (IPA) and maybe that'll get you something. But that is gene-level data and its probably not going to help. You can dig through PhosphoSite manually looking at the 163 sites that you found (or the 91 of them that have been annotated).
PhoSigNet is the ambitious endeavor of Menghuan Zhang et. al., to help us with this process. They have taken the data from PhosphoSite and CanProVar and other databases and ended up with 200k phosphorylation sites (almost 12k of which have been validated in one way or another!)
Through an algorithm that they call ExpCluster you can upload lists of your quantified phosphorylation data and it'll try to figure it out. Unfortunately, I'd have to dig pretty deep into my old hard drives to find a list of data to feed it (and I need to go to work!)
You can check out this awesome looking resource here.
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