Wednesday, October 5, 2022

FAIMS settings for ultralow (and ultra-ultra low flow) proteomics!

 


Do you have one of those big FAIMS things killing dewars of N2 in your lab...or...

...well...

...in either case, if your question is something like -- "Hey! What buttons would I press if I wanted to analyze <1 nanogram of peptide (why would you want to do that...?)?" And or "what FAIMS settings make sense for ultra low flow analysis?"

Check out this study where they worked it all out!



Tuesday, October 4, 2022

Study of DNA polyploidy cells is really a nice analysis of RNA-Proteomic correlations!

 


I started reading this because cancer polyploidy is really strange and very cool (honestly, I thought this was going to be background so I could better understand a recent paper out of Josh Elias's lab). Turns out the two things are only loosely related, and if I sort out the latter enough that my notes make sense, I'll come back to it later. 



If you aren't familiar with polyploidy, DNA divides in these cells, but the cells themselves don't. And some evidence supports them as being the origin of metastasic lesions. BIG DEAL. 

While I'm trying to force some new concepts into my tired old brain, there is a lot of this paper that is less difficult to grasp. 

Including some really exhaustive analysis of RNA to protein abundance correlations! No surprise, they aren't very good (the "correlations") but there is tons of great new stuff in this study, so the orange publish button will probably get hit. 


Monday, October 3, 2022

qPTM -- A nicely organized database of PTMs in some model organisms!

 


This wasn't the resource I keep dreaming of finding, but I do still like it


I'm not sure how this is better than PhosphoSitePlus and whatever the other thing is called that you can link to from UniProt now, except in terms of how it is organized. 

Think Mondays are a stupid day to read and just want to type something into a box? You can access this resource here. 

http://qptm.omicsbio.info/

Sunday, October 2, 2022

Saturday, October 1, 2022

Compare MS2 2.0 version 2 (dos, zwei, ni, tva, 'er, meiji, do, two, II)

 


Straight up, this kind of seems like some sort of crazy street magic stuff, but the nitpicky nerds that get to review for JPR let this one through, so I'm going to leave this here so I can look at it later. 


Weighting mass spectra -- across species? What the eff? 

Friday, September 23, 2022

UCDavis 2020 Proteomics Shortcourse is online?!?!

 

I'm always looking for great tutorials for the "Resources for Newbies" page over there --> and I just found out that the legendary UCDAVIS proteomics short course from 2020 is 100% online! 

I'll obviously add this to my list of resources but you can check it all out here

Thursday, September 22, 2022

Time to toss that nanoLC off the roof of the parking garage!

 

I've tried to hide my hatred for nanoflow liquid chromatography for over a decade now, but rumor is I haven't done it very well.

For more motivation to carry that thing up to the roof for real, I present a really nice study in JPR. 


In this work they pit a nice shiny Exploris 240 system with capillary flow (1 microliter/minute, which I'd still consider nanoflow vs microflow (50uL/min) in a variety of different contexts across multiple sample loads and total experiment acquisition times. 

It is largely what you're expecting --- peak shapes are better at higher flow rates, and lower flow rates do better with lower sample loads. 

Where all the work this team did really shines is in where you can get close to matching the coverage at these high flow rates vs low ones and you find these points where it seems pretty darned smart to use the 50uL/min. 

For example, for 15 minute LC runs, 2ug or 5ug sample load is pretty darned close at 50uL/min or 1uL/min. You could argue that was probably just too much sample for the little column used for the 1uL/min gradient, but still...we're talking about almost 2,000 protein IDs in 15 minutes! That's legit. 

Wednesday, September 21, 2022

Advances in Proteomics and Metabolomics 2022 by Tech networks!

 


If COVID-19 did anything for the world besides getting rid of a surprising number of people with the last name "Orsburn" it did, at least, bring digital meetings forward. So many opportunities to watch cool talks! 

I was just tipped off to this one and it looks great

Tuesday, September 20, 2022

Ubuntu summer school -- 5 days of proteomics in Antarctica!

 


Someone sent me this link to this very slow loading website where a ton of great speakers are teaching a summer proteomic school where there are penguins! As my public education didn't include a geography class and under the registration page there is a picture of an amoeba?....?...


....I'm going to make the uneducated guess that this meeting is in Antarctica. That's where my grad school roommate worked for 7 years but now got downgraded to working in the middle west somewhere. 

For real, if you want to see penguins and spend 5 days with some of the top proteomics researchers in thw world, registration is only open until October 14th! 

Monday, September 19, 2022

Study protein turnover IN VIVO in PEOPLE with DeuteRater-H!

 

"...because serial biopsies in humans are impractical..." (yeah...maybe a stronger word belongs at the end, but the point stands) it is really hard to truly understand in vivo protein turn over in humans.

So....what if you could talk an IRB (and some undergrads?) into having the latter drink deuterated water every day for a while and provide you with saliva serum and muscle samples here and there? 


Well...you'd have this study

Samples were analyzed on a tribrid Orbitrap system and to work out this new metabolic model, you'd need new software and you can get that here

Wow, right?!?!

Sunday, September 18, 2022

3 upcoming US HUPO Webinars!

 


Until recently I kept forgetting that US HUPO was a thing, it was even just outside of Baltimore a couple of years ago and I just forgot it was a thing until cool people started texting me to see where I was. This isn't a dig on US HUPO, we just got into some totally f'ed up traffic last week because I forgot that American football is still a thing and right after a match we were on the wrong side of a stadium from home and it took a really long time around people who appeared to be driving somewhat or incredibly impaired. 

Well, US HUPO IS a thing and they are putting on all sorts of great remote learning things all the time! There are 3 great ones of note in just the next 3 weeks! You can check them out and register here

Wednesday, September 14, 2022

16 proteomics sample prep methods head-to-head! The quest for the universal method!

 

If LCMS proteomics is going to scale up to the levels of new proteomics technologies that are willing to compromise specificity for throughput, we need to trim down the 4,512 different sample prep methods each lab has sitting around in stacks. You can't tell make a sensible argument that about 4,400 of them are unnecessary. 

What we need is some people to do the most boring studies imaginable just to get them out of the way. 

OMG. From the pit of my heart, I can't thank these authors enough for this study. It should be referenced by everyone in proteomics all the time. "What do you think about method A vs method B"? I have a hunch but nothing robustly tested but --- 


-- these awesome people tested them all! (Well...not all 4,512....but a whole ton of them!) 

Sure -- number of proteins are one metric -- but they ALSO break down the relative costs of the different methods! Proteomics sample prep has historically been pretty cheap from a reagent perspective compared to DNA/RNA assays that still require hundreds of dollars in reagents. But when you're setting up a 100 sample or a 4,000 sample study, those filters or traps and C-18 spin columns (and TRYPSIN) costs don't seem that irrelevant anymore. On a big study I recently realized that the 1:10 trypsin ratios recommended for some commercial kits was going to blow through every vial in our -20C in very short order. This group considered these factors! 

What wins? Nah, you gotta read this so you see how awesome it is. And you've got to remember to cite it later! 

Tuesday, September 13, 2022

No more Orbitrap Assend Leaks! Here is the full marketing dump!

 



As I'm looking over mostly completed blog posts and wondering why I didn't submit them, or removing completely unrelated gifs that make less sense than the ones I typically insert, I refreshed on the Orbitrap Assend official site and found tons of cool new information! (Working at a level that probably doesn't make sense in any possible way right now). 

This is old news for any of you lucky people who were in Maastricht, but for those of us waiting on the edge of our seats for every little Assend leak to trickle out, this big drop of information finally puts the hardware in perspective. 

There is a reeally cool little video at the bottom of the page with some gripping piano music that shows the whole ion movement from beginning to end for a typical data dependent experiment. 

(Please see disclaimers over there --> as always, I'm just trying to help get information out there!) 


Based on the architecture itself and what has been publicly released, the performance gains reported by Gygi Lab and Coon Lab are much better than I was expecting. This suggests to me that the obvious new fetures added (like a whole new multipole) aren't the whole story. There is likely some additional efficiency gains here and there. 

Honestly, on paper, I never expected the Fusion 3 Eclipse to be a big step up from the Fusion 2 for data dependent shotgun proteomics (I thought it was just for intacts and they'd kind of forgot about the DDA crowd), but when you actually process the data I have been impressed by the step up. It is easy to forget how complex modern instruments are and how little much little improvements like slightly reducing a gating time can lead to big improvements. 

Monday, September 12, 2022

"Next gen" proteomics deathmatch is published! Who cares about specificity?

 


Wow! Look at that, O-link looks great, see how it matches an error-prone protein quantification assay that we typically use when measuring as inexpensively as possible is the most important and accuracy is secondary? 

Oh. I particularly like this one as well! 


For my entry in the "most times I have literally laughed out loud while reading a peer reviewed publication while operating on less than 50 hours of sleep in an 11 day grant writing stretch "  I humbly submit --


Would you like to see my favorite funny part of this? To be fair, fate transpired to have my first solo grant application ever overlapping with 3 sets of really great journal reviewer comments all being due at the same time and my watch kept giving me this angry frown for my sleep tracker -- and I have had some sincere concerns about the quality of my driving on the beltway this week, so this might not be as funny next week as it is right now. (There's the period key! Looks like I forgot where it was for a second!) (Please, no real concerns about whether I'll die on the strech of my commute that we in the world's greatest city refer to lovingly as "THE THUNDERDOME" because, on a 5 year average approximately one person will enter per day who will not leave, when I'm really sleepy I drive my old stick shift car and it drives itself.) 

Check this out and tell me it isn't funny. 


Highlight 1 (my interpretation): Man, we're way more streamlined than LCMS! You should use our "next gen" technology if  you don't mind that what we're quantifying isn't SPECIFIC to the protein that we think it is. 

Highlight 2. Independent verification of our performance relative to a gold standard (I assume LCMS) for each of the thousands of proteins on these platforms is expensive and it will take a long time!

What comes to mind when you think about SOMASCAN and O-Link investors who are jumping on the proteomics bandwagon and are really excited about how much money these companies are spending on advertising their products because proving that they work is going to take a long time and will be expensive? 

Personally, I imagine that they're very tech savvy people who bring broad expertise in from whatever field they come from that readily translates to a deep understanding of any new technology!  

Time to change the topic to something completely different.

I don't think I've ever enjoyed a movie with Jim Carrey(sp?) in it enought to finish it. Even when he was seemingly in every 4th film in theaters I just found him completely unwatchable. However, I found this gif somewhere and I don't even know what movie it is from, but I have worn something remarkably similar to what he is wearing in this gif below. 

Wait. Is this the right blog? I should get some sleep. 

Saturday, September 10, 2022

IMSC2022 Final guest blog recap by Dr. Nick Riley!

 

Pop to part 1 or part 2 here.

IMSC 2022 Part 3: Wednesday to Friday

Wednesday, August 31, Day 3

Science Summary: It is difficult to pick between the best plenary/award talks of the week, but the Wednesday morning talks from Curt Brunnee Award winners Livia Eberlin and Erin Baker and inaugural Jochen Franzen Award winner Shane Ellis might have taken the cake. Following those, I saw great talks from Tami Geiger and Hem Gurung in the Translational MS/Cancer and Immunology morning session, and then chased talks between the Top Down and Imaging MS sessions after that. Wednesday saw a change over of posters (M/T vs W/Th groups), which brought more great poster discussions after a Thermo lunch seminar from Daniel Lopez Ferrar and Kay Oppermann about the AccelerOme. I spent most of my afternoon time in the second Glycomics and Glycoproteomics session of the week that featured interesting work focusing on structural characterization of both glycans and glycoproteins from Javier Torano and Cathy Costello, among others. I also was able to catch some cool real-time ID/quant work from both Gad Armony (Wessels group) and Chris McGann (Schweppe group). One of the highlights for me was Noortje de Haan’s talk in the Glyco session that showcased how glycogenomics and MS can work in tandem for O-glyco studies. If that sounds interesting to you, check out recent work from the Copenhagen Center for Glycomics.

 

Social Summary: Navigating the bus system in Maastricht is relatively straightforward, unless you assume there is only one train station. I confidently claimed a bus was going to the train station and led a group to the lesser-known, non-central train station several miles north of the city by mistake. I guess this is the price I pay for trying to only rely on free wifi at the conference center and hotel instead of double checking these things in real time with cellular data (which I eventually turned on). My bad, folks.

Culinary/Cultural Highlights: Erin Baker gave a nice (terrifying?) summary of how PFAS is everywhere, including our plastic food wrappers. It made the loud crinkling of plastic wrappers of the pre-packaged food during the lunch seminars sound that much more noticeable with a few more side glances than previous days. On a different note, the non-plastic-wrapped snacks and refreshments during the breaks and poster sessions seemed to only get better with each passing day.

Thursday, September 1, Day 4

Science Summary: A consistent theme here is the excellence of the morning award talks, and the presentation from Thomson Medal winner Vicki Wysocki was no exception. I unfortunately had to step out and miss the Thomson Medal talk from Lidiya Gall, but I was glad I at least was able to hear her present during the FeMS workshop on Monday night. Morning talks in the Biosimilars, Biobetters, and Glycoengineering session were mostly antibody-focused, with my favorite being the multi-protease approach to de novo antibody sequencing from Weiwei Peng (Snijder group). I also liked Johannes Helm’s (Altmann group) talk about PGC for isomer-specific N-glycomics and Mike Gross’s talk about different footprinting techniques, especially NanoPOMP, for membrane proteins. I spent my afternoon session in the second Young Mass Spectrometrist session, and each talk was impressive. If you are looking to know where the next generation of MS research is heading and you haven’t seen work from Karina Gonzalez-Estanol, Na Wu, Lieke Lamont, Guinevere Lageveen-Kammeijer, or Andrej Grgic, I highly recommend you check out their work.

Social Summary: The conference closing event was a fitting celebration of the science and scientists at the meeting. Set along a small harbor in Maastricht, it was an outdoor setting that underscored the good weather and fun city that IMSC 2022 enjoyed. I think this tweet summarized things nicely:


(Note, the time stamp is for my current time zone, not the local time zone where it was tweeted – I think.)

Culinary/Cultural Highlights: The couponed food was all pretty enjoyable, with one notable exception. Perhaps the Europeans will take issue with this assessment, but the trout paste “delicacy” was an acquired taste that several us had yet to master. Luckily, the other good food and non-couponed drinks helped clear the palate.

 Friday, September 2, Day 5

Science Summary: Similar to ASMS, if you stick around until the last day at IMSC, you are likely to enjoy some excellent science without as crowded of rooms. Still, I thought Friday was relatively well attended considering the jam-packed week it had been. Morning sessions included really interesting talks in the second High Resolution MS session that included everything from lipid nanoparticles to 18-plex TMT work on the Orbitrap Ascend, and the PTM crosstalk session and the second Imaging MS session also had full lineups of great presentations. The afternoon included a closing plenary and outlook for the next IMSC in Melbourne. To summarize the entire IMSC 2022 experience, it was quality science and quality social interactions from top to bottom. As I said in the first post, IMSC is now a conference that will consistently be on my radar.

 

Social Summary: I had a list of people I had wanted to catch up with or meet throughout the week, and a thinned out crowed on Friday morning helped facilitate a few meetings I was glad to have. I never really thought about it this way before, but for younger researchers who may want to connect with more established folks, these last conference days when everyone is a little less flooded with interactions from all sides might be useful. That said, beware that fatigue is real, and not everyone will be ready to have in-depth discussions.

 

Culinary/Cultural Highlights: The snack during the breaks between presentationso n Friday was vlaai, a Dutch pie-esque pastry, and it was amazing. Keep it on your list of food to try if you make it to the Netherlands.