Friday, June 23, 2023

Mass spectrometrists write unbiased study on why nanopores will never work for proteomics!


I do not know how I missed that this was out. I totally knew it was coming

It is easy to think sometimes that every scientist has their own preferences for what methods are the best and that this might, in some tiny way, shape their opinions on alternative technologies. 

That's just you being skeptical and negative, in my humble opinion.

And this study absolutely proves this point. Here, 5 experts in mass spectrometry totally got a nanopore guy to help them write a paper on why nanopores will never ever be a useful technology for proteomics. 

I imagine the writing meetings were like this --

With that out of the way, this is a seriously cool paper that digs deep into some of the fundamental aspects of protein expression dynamics in a really approachable way.

Edit here, because I felt like this comes off as too much sarcasm. I will reference this paper all the time. Breaking cells down to the per molecule level, as they've done here, is extremely valuable. It has gone in to the folder on my desktop for papers that I'll probably read over and over. 

At a pure molecular level, what would you guess costs more? An Illumina short read sequencing analysis? Or a 2 hour proteomics run? LCMS is the winner! might question the metrics used for comparison...because it was something like "which one would be the cheapest to measure 1 BILLION molecules"? Which really shines when you're like "how much would it cost to measure 1 molecule with this technology?" 

Therefore, if you had to choose a technology for measuring one single molecule, you'd obviously choose mass spectrometry, right? But you could see how an approach from another direction might come to different conclusions by shining a light on other limitations.

It isn't all nanopore bashing and vendor worship in this study at all. There is really great, valuable and insightful measurements throughout this paper. There is also some questioning of the role that mass spectrometry vendors have played in (limiting) protein measurement technologies. I mean...they have their motivations as well. I've had a really long month and being snarky is helping me kick off the last few minutes while the last grant application of the month goes out. The guy who learned grammar in Tallmansville, WV doesn't do the last round of proof reading. I get a few minutes. 

The study thinks about what lessons could be learned from each technology (mostly what mass spec can teach nanopore) and ways to circumvent the perceived challenges of where nanopores are today. 

Again, totally worth a read, and I'm not joking it is a really inciteful analysis. 

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