Sunday, August 5, 2018

PHOTON -- Is there finally a solution to phoshoproteomics signaling?


I made this statement twice in one week recently "what we'll give you from this experiment is a very large list of phosphopeptides and their relative abundances, and if you figure out what to do with it, please let us know"

BECAUSE I DON'T KNOW WHAT TO DO NEXT.

Sure, I can go to PhosphoSitePlus and I can see that my phosphopeptide has been found before and when (yay....)

Or I could pretend these are genes and put them into IPA and generate...well...something....

As a field, I think we've done a great job of ignoring this. Fixing it? That would be really hard. But -- I think that Perseus is sneaking in a solution.

Check this video out (did I post this before?)


There aren't loads of details on PHOTON outside of the video -- and here is where you can get the software to load into Perseus (1.6.2.1 or newer, though, I think this might be the newest). I presume there is a ground-breaking paper on the way!!

3 comments:

  1. Hi Ben,

    I couldn't agree more with you! Let me just add for the sake of completeness that PHOTON is included in the latest version of Perseus. The original PHOTON paper and the source code are already available. We are working hard on a manuscript that describes the latest additions to Perseus in detail. Stay tuned!

    Cheers,
    Jan

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  2. I guess PHOTON was actually published already: https://www.cell.com/cell-systems/abstract/S2405-4712(16)30369-6

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  3. Check out the Cell Systems paper describing PHOTON:
    https://www.sciencedirect.com/science/article/pii/S2405471216303696

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