Monday, October 12, 2020

STAMPS -- Build Metabolomics Assays From the Protein Level!


I'd love to have an argument with you about what "Metabolomics" actually means. To me, the sticker is that whole "-omics" part of the word. Wait. Terrible idea time. 

I'll argue all day that "proteomics" is only just now starting to happen routinely. Here is the argument, though, I'm not sure "metabolomics" is really happening yet. We know that only a small subsection of the metabolites in a cell will stick to reverse phase chromatography, and an even smaller section of those will ionize in one polarity and an even smaller section of those will survive ionization and out of those you'll confidently identify maybe 10% , maybe 30% of them?  If you haven't tried global metabolomics, give it a whirl. Then tell me how you figure out which of the 25 things confidently labeled as "inosine" is inosine. (The second one is probably hypoxanthine, it doesn't survive electrospray very well.)  

What was I typing abou....STAMPS! You can read about it here.

STAMPS dares to ask the question: "Why are you trying to quantify these frustrating small molecules, when you could be quantifying the proteins responsible for making and degrading them?"

And you say: "Because it would take me 3 miserable months to make the targeted assays"

And they said: "Oh. Here you go. We made them all for you." (In mouse, so far, but more is clearly coming)

This thing is super sweet. Go into the database and find the metabolic pathway you're interested in. (They've got 16,000 proteins in mouse available so far) 

Put a checkmark on the proteins that you want, right in the metabolic pathway for the thing you're interested in. 

Check the spectra of your targets, if you're interested. 

And download your assay. Formatted for input into Skyline! 

Is this still sorta targeted protein quan and not proteomics? Maybe. But if you've got the ability to choose from all the things, to me, that counts. I'll be even more pumped when they set up human, but if I was really interested it wouldn't be all that hard to port this with Picky or Phosphopedia or similar. 


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