Saturday, February 2, 2019
Machine Learning Reveals Protein Signatures for ALS!!
How'd I miss this one?!? It's 🔥🔥🔥🔥🔥
Nevermind. It came out in November. And I wasn't aware November had happened yet.
You can check it out (open!) here!
ALS is another one of those stupid human diseases that we don't put nearly enough resources into investigating and -- consequently -- know very very little about.
Time for some proteomics! (Hey! I know some of these people! Whasssup!?!? I love this study!)
Okay -- so -- let's complicate matters. How much do we know about CSF? Well...I know two people who are currently trying to figure out what the "normal CSF"-ome even is. So -- not a as much as you'd guess. Yes. This is 2018 and we still don't know what normal human body fluids are like. We'll get there.
How do you get over a hurdle like this? A LEARNING MACHINE and expert level proteomics.
In case you're interested in the proteomic data -- it's on Chorus and it's #1439.
It's what I know proteomics data is supposed to look like when it's coming off the instrument -- but -- somehow -- mine doesn't ever seems to quite look that way.
Sample #64...for example....(right? I know!)
The samples are Plasma and CSF from 30+ patients with ALS and 30+ healthy controls. The samples were depleted and digested.
A QE Plus instrument and -- fuuuuuucccck...... okay....you have to read this yourselves.....
....it's like a real scientist came in to our big fun proteomics science fair and took over..... Yes. This is awesome.
Despite the quality of the separation, you may be surprised to learn that nanoLC was used and the detector was a QE Plus. The CV of the plasma data is 1.6%. I was fine not knowing that the number could get that low. It was certainly better for my self-esteem.
Starting with this beautiful data -- everything then got more awesome somehow.
How do you do machine learning on a body fluid proteomics dataset? You break out the RStudio and you follow these directions.
I'm going to stop gushing over this paper and go do something else, but if you want an expert lesson in proteomics, or just an ego check, I strongly suggest you check this one out!