Tuesday, October 3, 2023



That's not news, I'm just having a good f'ing day. 

And I haven't just been not posting because the traffic here has been freaking me out --- 

Over 1/4 million views last month? That's stupid.  I've also had to prioritize getting papers out to prove to these grant people that we can do what we want to do next! 

Friday, September 29, 2023

Your last day to submit a workshop idea for US HUPO 2024! Abstracts open!


It's time to submit abstracts for US HUPO!!! 


As proven by Ben2 and Brett's awful LFQ Battle Royale Workshop, they'll let anyone put them together. I really just applied for a workshop because I had these hilarious old pictures of my workshop cohosts and i wanted to submit them somewhere and - BOOM - we had a standing room only workshop!

Reminder -- in 2 weeks we'll do round #2 of the Battle Royale open to anyone in the world to see how global proteomics quantification methods stack up. Register here! 

BlueSky Social Week #1 -- Twitter without gifs -- and ads - now BioRXIV support!

 Article here

First question -- BlueSky is by invitation only and, no, I can't invite you yet. I haven't been on the platform long enough to invite anyone, but if you were looking for #MassSpecTwitter and for the coolest papers, Mastodon and BlueSky have them.

I need to figure out how to get into Mastodon again and see how it has evolved, but I might already be following more scientists on BlueSky than I ever did on Twitter. 

I did put one post on Twitter this week so I could amplify a student's 63 page paper (!!) he submitted and posted on Biorxiv since Altmetric tracks Tweets but does not yet track reposts on BlueSky, but with bioRxiv joining the party, it's only a matter of time. 

Thursday, September 28, 2023

Question everything? Sensitivity tailored DIA for single cell proteomics!

Woooo! Okay - so there have been some surprises in working with actual human cells that everyone is running into as their getting going. A lot of the things you know will work from your years of doing proteomics with basically unlimited material....don't seem to work quite as well. 

And this great new paper goes through a lot of these surprises.

For bulk proteomics we've been trying to get to faster and faster instruments so we can get to smaller and smaller isolation windows, particularly for DIA. We also know from - forever - that longer gradients basically lead to a linear increase (not a 1:1 but I think it's still a line, there probably is a word for it, but I've got a bunch of deadlines) in peptide identifications. 

Check out the image at the top of the post - doubling their gradient gets them what? a 10% increase? You doubling your acquisition time for 10% more peptides? Me either. You can look at the window optimization inside, it's cool stuff. Also -- gas phase fractionation (where you make libraries on an system by doing DDA on little narrow windows of your samples, for example only doing DDA [or, I guess, DIA] from 400-600 m/z, then running that sample again and only doing 600-800 m/z, etc.,) has a lot of value. 

The coolest part here is the biology as they track the proteome of this cellular population as their differentiating. We're getting out of the methods development side right now and it's time to start rewriting some text books (or whatever they use now). 

Wednesday, September 27, 2023

Make beautiful figures out of any spectrum from any instrument with this easy online toolkit!


I didn't want to post anything on this super cool new online tool from Goodlett lab until I had all my figures made. Don't want to Orsburn Effect something that I need for a deadline and talk next week! 

Do you just want to take a mass spectrum from anything - maybe even different instruments or online data or NIST fragments or literally anything else and just make a nice figure? 


Feel free to read the nice tutorial - or just use the most intuitive interface you've ever seen. 


That figure at the very top is me extracting diaPASEF data from a drug standard and from a drug treated complex sample! Bottom is my drug standard. 

How do you do this? You get into the hellscape of terribleness that is "Data Analysis(TM)" and you find your spectrum and make it a "Compound Spectrum" then you right click on that spectrum in your table and export it as a peak list .ASC file. Then you open that in Excel and trim out the 3rd column that is just random weirdness, save it as a .text file and load it into www.mass-spectrum.com.

You can add an Excel file with your masses/peak lists and - BOOOM - you've made a labeled plot. Everything from the colors to the fonts to - you name it - is user selectable. 

I've successfully made a mirror plot from QE PRM data for a standard small molecule and from a TIMSTOF diaPASEF small molecule run! 

EvoSep Webinar 9/28 - Is this the OneTip unveil? Digest, clean and load on 1 EvoTip?


You've probably heard rumors (and maybe there is now a preprint, I can't keep up) that there is a method for directly dropping your cells onto an EvoTip and then digesting them there, cleaning up the digest and then just directly shooting into your instrument? 

Don't quote me, but I suspect this is where we'll see it. 

You can register for it here!

Tuesday, September 26, 2023

InstaNovo - Can neural networks make real de novo peptide sequencing a reality?


Full disclaimer - I can't follow all the words in this new manuscript. It is very computer science term (?) heavy. Honestly, if I hadn't found on page 35 that this code is available it wouldn't have made it on the blog, but from the proteomics data I can follow it looks really promising.

If you're a computational nerd person, I think this is what you want (Github). 

From what I can get, at very reasonable FDR, InstaNovo is identifying as much as 50% of human peptides that are known - with no database at all. None. Sure, having a database for something you have one for looks better, but this opens up a tremendous number of things that we don't have sequences for at all. They pressure test this with less used enzymes (GluC) and do some HLA/MHC peptides and some mixed proteomic samples (metaproteomics). 

Monday, September 25, 2023

"Alternative" careers after your degree! -- US HUPO Webinar tomorrow 9/26 at 1pm EDT!

HEY! You're getting a degree in some academic lab! Great for you! I bet everyone around you where you're putting in a very rational number of hours to get that degree has insight on how to best be an academic.

Does it feel like  

? Probably does, right?

Of the people I started my PhD program with, there are very very few people in academia right now, and I went and did random stuff for like 10 years before coming back. There are other paths. Most of them will be other.

US HUPO has a thing tomorrow talking about 2 you probably never knew existed (I sure didn't).

You can register here

Sunday, September 24, 2023

Ummm...single cell lipids at analytical flow rates?


I'm....very very surprised by this one, y'all. Legitimately I feel like I'm off an order of magnitude or two, but this study seems well thought out and the results look okay on the surface. 

And this looks just....sophisticated enough to be something people would do single cell analysis with

This group used a standard QE Plus operating at 300 microliters per minute (or 350 microliters/minute if using a special column) -- holy crap. I wouldn't have guessed I'd have detected lipids in 1,000 cells. Let alone one at a time. I've got a QE Plus! I'm pretty sure the LC on it can go that high, I generally run it lower so I can have higher sensitivity, though...

Now....apparently the reviewers at ACS did forget to make sure that the RAW files were publicly available, but maybe they don't require it because who cares about lipids? 

Okay, because I have a rapidly approaching deadline -- what is the lipid content of a single cell anyway? Table 7.1 in this old book (open access here)

5% of the Eukaryote cell content is lipid (probably put a big -ish on this, I can't find the original study of Alberts, 1983 through the references). So....let's go with that's around 50 picograms of lipids per Eukaryote cell. Okay, at least it is more than the 1pg or so of mRNA floating around (about 10% of RNA is mRNA, most of the RNA around is the stable stuff, 16S, etc.,) I'm getting that number off of it being about 1/4 the percent content of protein and a mammalian cell is generally around 200pg (blog post from 2014....ouch...wait, I was still using SpongeBob memes in 2014?) 

What about their standards? They used the ones we use from EquiSplash and they optimized at 16ng/mL

So, 16 picograms/uL and they put about 5uL injections, so they optimized their method around 80 picograms.

That's not too far off the 50 picograms per single cell, except that's total for phospholipids and other lipids. And since I have no idea what the distribution of different lipid species are (how many and do classes 1-7 make up 90% of them) but -- this actually seems like it is in the right realm order of magnitude or two. Weird, right? 

Single bacterium proteomics!

Wooooohoooooo! Okay, so I mentioned that this was coming during my barrage for ESCP in Vienna, but it's already out! Told you, JASMS is on fire right now.

This is a SCoPE-MS style study with single E.coli. Yes, something like 1% the size of a human cell. 

You should check it out. My kid has a potato and he won't stop screaming "I HAVE A POTATO" until I acknowledge this fact to his satisfaction. Really exciting stuff in both the paper and this ready-to-microwave Russet.