Tuesday, April 11, 2017

Tumor xenograft RNA-Seq, proteomics & phosphoproteomics integrated into a solid story!

I don't know enough about cancer biology to really dig into the results of this great new paper...

...but I know a goldmine of valuable cancer information when I see one!   

This study is big. Like 40 tumors grown in mice --> excised, and then put through RNA-Seq, iTRAQ4-plex proteomics and label free phosphoproteomics. It is a lot of data --more importantly,  it is a lot of publicly available data!

The best part for me is the level of integration from the different analyses. This works out to be a cohesive story with phosphorylations that are present making all sorts of sense in terms of the proteins that are regulated by that phosphorylation, or the transcripts that are coming up before the proteins can be translated.

All the proteomics was done on a Q Exactive Classic. Data was processed mostly in MaxQuant, though Spectrum Mill was also used to integrate the proteomics and phosphoproteomics. 

This study was obviously a load of work, but it was executed really really well. Don't believe me? If your institutional firewalls will allow connection with Aspera, you can get all of this data here!

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