Thursday, April 11, 2024

How fast is a Mac M2 chip for proteomic / scientific data processing?


I recently had a Windows PC perform an unauthorized system update in the middle of a big batch of files and gave up and bought my first ever MacIntosh/Apple computer. Possibly because I grew up in somewhat extreme poverty and possibly because I don't particularly like the color silver, these things always seemed like they weren't for me. But they are advertised as very very fast. 

It's easy to be skeptical, though, because now they are making their own chips. They can use whatever benchmarks they want. The benchmarks I care about are processing proteomics data! 

TESTING TIME! My Apple M2 Pro with 16GB of RAM and 1TB hard drive vs my closest looking Windows PC - same number of cores, but Passmark thinks it is a little slower. 

First experiment, performed between when my elderly dog needed to pee at 3am and when my toddler woke up at 5am. Details are fuzzy....

Tools - SearchGUI with MSAmanda 3.0 and SAGE

Random HeLa digest file from an Exploris 480 with FAIMS. 200ng separated over 120 minutes on an EasySpray 25cm x 75um with a 3cm PepMap trap. Converted to MGF and having around 110,000 MS/MS scans. I might have generated it or downloaded it. Not sure. It was on my hard drive from this review I did a while back. If you want the file the MASSIVE download link is in it. 

Search tolerance was set at 10ppm MS1 and 10ppm MS2. I used the Uniprot Swissprot for human (9606) that I downloded this morning. 20k entries and I had SearchGUI add decoys. M+oxidation and static carbamidomethylations (these are the SearchGUI defaults).

Windows PC - pretty freaking fast at 3 min and 25 seconds! 

M2Pro -- 

2 minutes and 5 seconds! WHAT? Not the way I expected that to go. 

Okay - I should also point out here that SAGE is nuts. But the discrepancy is even more insane on the much new MacIntosh chip. 13.4 seconds to search a file vs 2.9 seconds to search a file?? 

Then it occurred to me that it's probably not fair to run a file on a MacBook on a battery. I plugged it into the wall, deleted the first output file directory and reran the file.

Maybe a tiny bit faster, but within the margin of error here? 

It is fair to note that the Windows PC I'm currently typing this on doesn't do much data processing these days. It's certainly perfectly suitable and I have zero reasons to think I'm not going to be using it as my primary office PC for several more years. However, for our main PC "server" which has supported as many as 6 users with SpectroNaut, Proteome Discoverer and Compound Discoverer we've been using a Ryzens 9 (I think this is the chip on that box below) - which aren't even all that fast now! The big EPYCs and Threadrippers are pushing 3x this benchmark - but you've got to be ready to drop as much as $10k just on your processor. Good time to be a consumer if you need PC power! 

That was a lot of words, for - hot dog - these Mac chips (and SAGE! WTF?) are FAST! 

Monday, April 8, 2024

Is a TOF killing technology on the horizon? TMT32-plex looks official!

We saw a leak to potential investors of one of our field's oldest and most ethical companies stating that a 32-plex was coming. Not a "I SILAC'ed it and TMT'ed it" technology, a real life reagent that would allow you to multiplex 32 samples simultaneously! 

While the expectation is that we'll see real details of these reagents at some thing in Anaheim in June, one core facility is already advertising that they've got it. You might be able to guess which one, but I think it's fair to say that it is really truly real now. 

Short of completely redesigning the tags there are only a couple of ways that this would be able to work, right? And I can't think of a way that you do this without requiring an increase in the relative mass resolution necessary to use the tags. 

For some people this might not be a big deal, right? There will probably be some drawbacks, like the whole "now I have 32x more albumin to deal with instead of 18x more albumin" but for some of us this reagent could be completely transformative. 

This is how we multiplex single cells in our lab (from Eberhard and Orsburn, which should be out any day now) using 2 x 96 well plates for 2 conditions. That leaves us with 16 unused wells per plate, which is what we use for LFQ single cell method development. Anything you see out of our group like the acetic acid preprint or our upcoming miserable work with 20um ID columns, is done using the 16 cell left over from the hundreds of plates we have went through the last 3.5 years. 

32-plex will allow us to switch to using 2 x 384 well plates! know what is crazy? This actually almost makes it easier for me to automate. I just have to fabricate a new sample deck that will allow me to stack my plates sideways! 

Sunday, April 7, 2024

Confuse everyone by converting an EvoSep One into a fraction collector!

If you've got a spare EvoSep One sitting around not doing anything you could sell it to me for less than a new one costs OR could get a 3D printer and convert it into a (??) ... robust and sensitive offline fractionator.

The 3D printer converted to a fraction collector is seriously cool.  You can get a shockingly high resolution 3D printer for <$500 these days and you won't need super precise movements to put your tube above the right well in a plate. Steal these plans to build your next fraction collector, for sure! 

The...use of an HPLC system that costs the same? more? than an HPLC with an integrated fraction collector...likely makes this more of a niche idea. The sensitivity is really good, though, with good recovery of high pH fractions of 5ng of tryptic digest. 

Saturday, April 6, 2024

Moms in Proteomics pushes for change!


If I knew about this, I forgot about it somehow, but it came up on a cool podcast recording and now I have the link. You can check it out here!

...or this article! 

Or this original article! I've clearly been living under a rock or something.... What super cool ideas all around! We all know that proteomics will inevitably become the most imporant -omics. Making sure we have support systems for all of our scientists now is the way to make sure it happens sooner and is sustainable. 

Friday, April 5, 2024

New THE Proteomics Show podcast with - Dr. Henry Rodriguez!


B-sides is the new "season" of THE Proteomics Show where we just have guests that we've really wanted to talk to. Henry Rodriguez has been on my list for a long time, even before he held a position in the WHITE HOUSE! 

There probably hasn't been a stronger advocate for proteomics - as a science - in the US government and it was super cool to get his side of the stories - like how did CPTAC get started?? 

Thursday, April 4, 2024

I'm walking into spiderwebs - making sense of protein-protein interaction data!


For maybe the most creative abstract/TOC graphic you'll see today - 

I legitimately laughed out loud when I saw this new paper ASAP. When Ska went mainstream in the late 90s, I was NOT a fan, but it was absolutely everywhere. You couldn't avoid it at parties and I WAS a fan of parties in the 90s. 

More importantly, this paper is really super useful! Who doesn't have a protein protein interaction network on their desktop they are saving for a day they have nothing else to do and feel really really smart? There might be 10 on mine that I'm not entirely sure what to do with, but an answer might actually be in there somewhere. We have some compelling and very confusing FANCM enrichment data that I've looked at off and on for months. There is something in there, I have no idea what. 

And in case you aren't in your 40s, this is what this TOC graphic for the paper might be inspired by. Maybe. The single from that album was called something something spider webs. 

Wednesday, April 3, 2024

Reinvigorate that older hardware with second party ion funnels!


I'll leave this here without much comment, but pulling off the front end of an Orbitrap Velos/Elite system and putting in a dual stage ion funnel sure seems like a smart way to keep that depreciated instrument contributing. I feel pretty confident that I can guess an application this might be applied to by the corresponding author's exceptionally innovative group. I'll be on the lookout for it! 

Tuesday, April 2, 2024

SpectiCal - Use those low mass fragment ions for something!


You know those low mass fragment ions your search engine is probably set to ignore - because - let's face it - how useful is it to know there is a protonated lysine fragment there? 

SpectiCal will take mzmL files that have these things in them (they all do!) and will use it to recalibrate your MS/MS spectra! 

We recalibrate all our TOF TMT spectra using the reporter ion exact masses using a lousy program I pulled together, but it is very manual and - not useful for something that isn't TMT.

This is dynamic and - while it has the dreaded "pip" in this Github, that's something ChatGPT can help you with if you're not sure where to get started. 

I presume for Orbitrap spectra you could start talking about ppB mass accuracy after running it through something like this! For me, I just want Orbitrap level accuracy at (affordable) TOF speeds. 

Monday, April 1, 2024

Two sources appear to leak details on new ASMS hardware! Booking a flight to Anaheim now!


Honestly, I don't think this is anything that will come as a surprise to anyone at all. Particularly if you have taken a look an realized how very very old the Trapped Ion Mobility patent is (2008!

The first came to us out of Australia, by way of 

Full text here! Honestly, my first thought was "why not Ultra" but Flex obviously makes sense, since Thermo doesn't have MALDI capabilities. And since Bruker can't get pasef to work with MALDI, Asstral backend makes an awful lot of sense! 

Just a few minutes later we had this release suggesting the obvious - that Veridian Dynamics -  is involved in this collaboration. 

While we haven't heard much from VD recently, they were the first to jump on the expiration of the Orbitrap patent and begin commercial construction of their own hybrid devices! 

Given word choice on the Veridian release, I think it's safe to say that one of our leading labs is involved in this! 

Guess I do have to work out travel to Anaheim afterall....biggest year for $,$$$,$$$ level mass spec labs ever! 

Wednesday, March 27, 2024

Aftermarket high resolution FAIMS allows separation of MEGADALTON protein complexes!


FAIMS gets a bad wrap because most of the commercial systems have a resolving power of something between 5 and 20. They're great systems if you just don't want to fragment (or see) +1 ions and you want your mass spec to only see +2 or +3 ions. Cleans up your spectra so your mass spec doesn't have to work as hard, and everyone is happy at the end. that a limitation of FAIMS technology itself, or is that what is mass 😁 produced for the general market? Sure sounds like it's the latter. 

In this new study an aftermarket/custom high resolution FAIMS system was coupled to a UHMR (which has an upper mass limit of 80,000 m/z? Is that right? That's huge) and oligomers of antibodies (so a monomer is around 150,000 Da!) were coupled. 

The study is maths heavy and there are a lot of formulas, so I found it hard to get to the effective IMS resolution. However, this 2019 study indicates that the FAIMS is >100 resolution, and I think the two devices are similar

And - get this - you can get this FAIMS system for the front of just about any instrument and they can be custom tuned for small molecules, peptides, or intact proteins. And they're a lot less expensive than the 10 resolution units that you can buy for only certain instruments.