Wednesday, November 8, 2023

QuantumESSI writes least biased app note in history - bye bye LCMS, Ploopinum time!


This week I was thrilled to find that 8 new emails from newcomer QuantumSi informing me about their head to head battle with LCMS.

I was even happier to find out I had to go to their site and fill out a bunch of stuff about myself in order to access this app note. 

Possibly the greatest moment of my life was reading through what appears to be a high school student's interpretation of the experiments that were performed. It wouldn't have been at the pinnacle of my life's experiences without the requirement to agree to be Added. To. The. Mailing. List. to download it when I clearly followed one of the 8 links handily provided to my inbox because - presumably - I'm on the mailing list....

9th time's the charm, right?

Here are the details on the mass spectrometry

I don't know who did this for them, but - bravo - 5 day turnaround - including however long it took them to ship it to you? 

The Ploopinum system takes about 4 days including digestion, the 10 hours the sample spent on the instrument in their lab, uploading the data to the secure cloud and - presumably - doing cloud things on this single purified and digested protein.

But it outputs prettier data than the core did! Look at this! 

Just about every LCMS core has different levels of data that you can provide to collaborators/clients right? The phenomenal core at Pitt has "data processing tiers" and I think that is a smart idea. Some of my collaborators want to install the Proteome Discoverer viewer on their PCs and actually look at their data. Others, however, want a protein list like the one at the top. I'm lying, of course, I always offer the viewer software and processed data and in 3 years at this university no one has wanted it. They want the spreadsheet. 

Takeaway number 2 ? The Ploopinum isn't fast. Even if you have one in your own lab, for your purchasing of this box, the reagents and the cloud subscription service and the dedicated operator to do the experiment, you're slightly faster than an LCMS core service.  (Takeaway #1 is that this company's marketing could use some work).

Okay - but why is the Ploopinum so superior? That's the whole reason you're reading this, right? 

The Quantum device identified 2 peptides that the LCMS analysis did not. 

The first was a 5 amino acid section RLYCK (this was a LysC digested protein) because the operators only considered a 6 amino acid or longer region to be worth reporting to the end user.

You could argue, I guess, that the reason we ignore chains of 5 amino acids is that they are generally quite likely to occur at random throughout the proteome of anything - like, for example, the amino acid combination RLY is found in 11 proteins in the cRAP database. So....I ain't reporting that I found an RLY peptide to anyone. 

RLYCK occurs in 4 human proteins in the tiny canonical (no isoform, no common population level genetic variants) UniProt/SwissProt database. (It occurs 14 times if you consider common human single amino acid variants deposited as of the last time I updated my library in 2020). UniProt matches shown below. 

So...if this was a "proteomics" service request, most facilities won't report this peptide. 

And the Ploopinum identified a peptide with a pyroglutamic acid in it that the LCMS core did not.

Of course, the LCMS core was able to identify that peptide when they were asked to look for it and you could argue that it seems a little suspicious that the core appears to have been provided a purified protein and was not asked to look for PTMs in the sequence - like...maybe this went to a proteomics core and not to a facility that specializes in single protein analysis? ....but it's too late. The damage has been done. They handed this data to Billy and he already got a C on his writeup for his 9th grade general science research paper.  Someone in this company who wears a suit every day said "looks great Billy....let's not put your name on it, though, and the best way to get this marketed to the right people would be to send it to people with LCMS systems!" 

It worked! I've already powered down my mass specs that weren't destroyed in our most recent flood, because clearly this little instrument that takes 10 hours to identify 8 LysC digested peptides from a purified protein is the future. (OMG. Because some people can't tell when I'm being saracastic, no I'm not powering down any system here. On my oldest system -- that is no longer even manufactured - an S-Trap digestion of this purified protein would be about 2 hours (about 12 minutes of work) and I'd run this on a 20 minute LCMS gradient. I'd run it through single protein analysis software - NOT proteomics software - and I bet you I'd have better coverage of this protein by the time I'd forget to eat lunch today. But not everyone has this stuff around. And you can't get a degree in proteomics. You have to learn it on the job. 

Now - I've been pretty negative about this, but I tell you what, there is at least one of these things on the way to my university now. Because this little box has a lot of potential for researchers with a lot of money and without a lot of patience for me and my whining that my I need consistent temperature, relatively consistent humidity and dry floors in my lab to operate my mass spectrometers. There is a market for this little box. Despite the 9 emails I'll get every time they write up every app note, it isn't marketed for me, but it certainly will find homes in labs out there in the world. 

1 comment:

  1. I appreciate you making the effort so I don't have to :D