Another older one -- THE guide to structural elucidation of small molecules!

 

Some people do proteomics all the time, and that's enough to keep them busy, but I bet most of you get asked if you could work out some weird molecule or someone runs into your lab pleading for you to tell them if is this a really high level of pesticide in the serum of these people??" If you're smart, you'll turn it down, but if you're less smart or just can't say no to anyone who sounds smart, you need some solid resources to fall back on --and in my ever humble opinion is THE guide for solving a small molecule.

It might also be a who's who of unpronouncable last names....

LFQ Analyst -- Another great downstream data interpretation web app!

 

I swear I'd talked about this one here before, but can't find the post anywhere....

There isn't a paper for this one yet, but I've head a rumor that it's coming. This is from some place called Monash where rumor is there are some people who know about bioinformatics.

LFQ-Analyst is really stright-forward for MaxQuant uploads and generates some nice solid visualizations. I've been assureed that other direct data import tools are in works as well. 

You can try it out here! 

Affinity Enrichment is nearly always better than (attempts at) Affinity Purification!

This paper is older, but if I send the same link to a study to three people in under 2 weeks maybe it's good to talk about it again! 

Biologists do tons of "pull-down", "immunoprecipitation", "immunoenrichment" things from the simple to the "number of steps that don't even seem remotely possible to pull off but is for some reason absolutely acquired to find this target". 

Despite how they set up the experiment, there is something for them to learn from this paper, particularly if they haven't done an experiment like this in 20 years and are expecting a short list of presence/absence. Now, I'm much more likely these days to send out a report from FragPipe for quantitation, because it now has match between runs and match between runs FDR and I can have a saved template for "so and sos triple knock out mutant IP" because I'll always forget at least one setting in MaxQuant from the last time I ran it, but the principle is the same. Simpler + better semi-quantitative = better. 

That is the first paper I send them. 

The second thing I send them is from a great little proteomics core lab at Colorado State University. Here is a direct download link for this PDF. It's called "Detergents in Mass Spectrometry" and it's important. 

Definitely definitely definitely keep this in mind -- A few years ago some biologist got the great idea to start washing IPs, etc., of detergent used to lyse the cells with the exact same detergents used to lyse the cells. I believe this to be the most popular idea in all of biology of the last 40 years because EVERYONE does this now. The uptake from isolated occurrences to ubiquitous has been mindblowing. I don't think PCR caught on as fast as washing detergent out of things with detergent. As far as I can tell, every person that I've been able to catch in the act (or....after I've spent loads of time removing Triton X-100 or NP-40 from an HPLC....) has experienced zero ill effects from just removing the detergent from their wash solution and following that protocol to the letter. 

Why don't we just stuff a nanopore into a mass spectrometer?

 

Nanopores are great because you can push a nucleic acid polymer (or protein) through them exactly one monomer unit at a time, then you can look at what comes out one at a time.

While the separations are super cool, the detection devices are -- from the perspective of someone who regularly utilizes neutron mass discrepancies to quantify things -- meh. 

What if you were to couple what the one thing does well with what the other thing does much much better (with the exception of leucine and it's dumb isomer, I guess)? 

You'd have something like this: 

For a really thorough walk through of how this works, there is a video from SCP2021 here! 

For some context, you have to put the nanopore emitter into the instrument. And the size of the pore is about an order of magnitude smaller than the nanoESI emitters that we typically use, but the potential sensitivity gains are absurd. 2 orders is potentially out there. 

Amica -- A simple and intuitive data interpretation program (and website!)

 

There is an ever-increasing number of nice tools for getting from that annoying text file of results so some sort of biological interpretation. 

Amica is a brand new one that is definitely worth taking a look at!

While the first thing to catch your attention might be that you can directly upload your FragPipe output, you might end up staying for the pretty plots. I particularly like intuitive and interactive PPI plots like this one.

I feel like the majority of nice Shiny type tools out there for proteomics need to have columns all moved around for anything other than MaxQuant (which this also directly accepts) but the increasingly large Fragpipe user base should direct a decent amount of traffic to this great toolkit.  

You can play around with formatted example data on the Amica webpage here without downloading anything! 

A gigantic LFQ modeling dataset comparing just about everything!

 

Need some files to compare between different instruments or to test your pipelines? This recent preprint probably has you covered. 700 instrument files with tons of replicates and QCs! DDA vs DIA vs fancy things are are DIA with little tweaks and funny names? It's all here! 

MhcVizPipe! QC Software for Immunopeptidomics!

 

Huge shoutout to Dr. Neely for tipping me off to this new study and tool! 

One of my favorite takeaways from this year's ASMS was the amount of precision targeted work that was going on with HLA/MHC peptides. By now just about everyone has been on some project to identify as many of these poorly fragmenting frustratingly low abundance peptides. Here is the turning point, though, groups doing studies like this one and this one are TARGETING important peptides coming from these lists and developing actionable therapies like this one I raved about a couple weeks ago. 

These studies are absolutely no fun whatsoever for the person doing the sample prep, running the instrument or processing the data. One thing that has been missing has been any real way to QC your experiments or results before letting your software of choice spend FORFREAKINGEVER digging through your data. Is MhCVizPipe the answer? I don't know, but it sure looks smart! 

I send anyone who asks for this stuff to.....oh...fuuu... Okay, well, I used to have a place to refer anyone who asked but I think there is just a beautiful empty lab there since everyone there was recruited to industry.... Well, maybe I will find out soon! 

8k proteins/hour in 3 samples with multi- plexDIA on a QE "Classic"?!?

 

Hey you! Do you think you need that new ultra-expensive fancy pants instrument to compete with today's flashiest hardware?  It might seem like an unending rat race in a field largely driven by instrument vendors who somehow maintain possession of the ever-dwindling supply of real mass spectrometrists (the ones who have built or significantly altered instrument hardware before, which is a distinction in some branches of mass spec, where the rest of us are "users"). 

Or. Have we still not tapped the full potential of instruments that are rapidly approaching a decade out in our hands? 

I'll leave this here. 

I have never once in my life gotten anywhere near 8,000 proteins in an hour and I've got access to some flashy new stuff these days. 

All the files are open on MASSIVE here!

All the ASMS posters are open for everyone at no charge today and tomorrow!

 

Hey you! Are you bored at HUPO? Are you not attending HUPO, but want to see tons of ASMS posters? 

Today and tomorrow anyone with an ASMS login can go and see all the posters! You can check that out here.

Human Proteoform Project! Let's go!

 

Okay, so here is an initiative that we should all be excited about! 

This extremely well-written and concise review is something we should be sending around (if your facility isn't already operating at 200% capacity thanks to all this new excitement about proteomics!) to justify those top-down focused instruments! 

EggNog-Mapper V2 -- Updates for Meta(Prot/Gen)omics!

 

This might largely be for me, but there are some metaproteomics people out there! So many that they just had a conference, I think! 

Ever just ended up with a big batch of de novo results or matching your proteomics data to some RNASeq /PacBio or NanoPore data and instead of getting an accession that is useful you just have 00034634543563459054P0000P203940938430294 and thought about pBLASTing every one individually to figure out what the heck it does? 

DON'T DO THAT! (I mean, do what you want, but after the 10th one I bet you'll be rethinking the missteps you've made in your career that led you to that moment). Then Egg-NOG it! And there are some amazing new updates for it. 

A rigorous evalution of COVID-19 peptide targets!

 

After dumping a relatively large amount of time and personal funds into SARS-CoV-2 peptide detection early in 2020 (and subverting some great people to help me!) I ended up with some COVID research fatigue. I know people are still doing great work out there, and here is a nice recent example! 

If you also have some fatigue but also curiosity about targeting the virus, this group goes back to the beginning and critically reviews what work, didn't work and why and fills in a lot of gaps for any future work toward viral detection. 

Somebody pulled off protein sequencing by nanopore!

 I've got almost as many unfinished blog posts as manuscripts open on my desktop and some pressure to wrap up some things before others, but -- holy cow -- this is fantastic! 

Not only do they pull off sequencing a protein, but pull it back in reverse it to do it again! Full de novo single protein sequencing from a single protein molecule. Sure, it's slow, but have you seen their solutions for speeding up their DNA sequencers? 

I only x'ed out the one that, in my ever humble opinion, is dumb (it's a cheaper version with too many limitations to make it useful for anything I can think of). You can plug your single sequencer into your laptop with a MinIon (I only have an older one and its a little big for a thumb drive. Think about 1/3 the size of a small iPhone) and if you need to do more sequencing you can plug a bunch of them into a GridIon and plug that into your laptop. And if you need a crap ton of throughput you can plug several hundred of these things into a big box called a PromethIon. 

"In-cell" digestion with MS1 matching!

 

Gotta leave this here to make sure I don't forget to spend more time on it and forward it around. 

ASMS Day 1, my rolling record of some of my favorite posters!

Here are some ASMS posters that I've really liked so far (this might keep expanding as this is where I am keeping some of my notes). 

MP321 -- Using a TMT method called Tomahto to go after "Dark kinases" (did you know we still don't even know all the kinases?? WTF?

MP312 -- A really cost effective looking way to multiplex up to 32 samples

MP331 -- Depleted and TMT10-plex labeled high pH offline fractionated plasma from diseased children. One of the deepest plasma proteomes I've ever seen. Pretty downstream analysis

MP345 -- Whoa. TMTc looks really stellar compared to even MS3 based quantification? I need to hit this group up for some help with their Github stuff. 

MP348 -- Someone actually did the video upload! Understudied organism (lake trout) brain proteomics? in the context of evolution and polution accumulation? Impressive work and from an undergraduate researcher! 

MP333 -- A new TMT QC standard! I love the TKO standard! This looks to me like it's the TKO standard taken to a whole new level with quantification involved as well!  Wait. WTF is Proteome Discoverer 3.0? 

MP051 -- An absurdly pretty histone marker analysis! 

MP041 -- Luxon (the laser electrospray thing) analysis of serotonin in plasma

MP017 -- A great argument for serum glycomics!