Wednesday, April 28, 2021

Neat integration of TMT phosphoproteomics with transcriptomics!

The effects of my over-exposure to Arabidopsis from my years at an agriculture focused universities might finally be fading a little. Or this great study from last fall beautifully demonstrates something I've aspired to pull off myself and never have this well, and if you can pull it off in this awful plant, you could apply this to interesting things! 

If you don't want to read the preprint from the figure at the top, here is the hook.

There are a lot of studies out there that have brought together proteomics and transcriptomics. Most of them have required a bioinformagician on the team to pull it together using a series of tools that I am probably not smart enough to install.

TMT-NEAT, however, is a perfectly packages Shiny web application that you point at your MaxQuant output files and it pulls your data together.

To this day, virtually no tools out there autonormalize your phosphopeptide abundance to your protein abundance. That's why this lazy tool I made gets downloaded from the blog so often. TMT-Neat does this directly from the MaxQuant output files and does it the right way, not the lazy way! 

Honestly, I'm guessing we haven't seen this paper in print yet because it's going to be in a big journal soon and I don't even think that what I'm impressed with is why it will publish so well. The majority of the paper is focused on what they actually found, which seems like kind of a big deal. I hope the reviewers at least appreciate the informatics. 

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