Thursday, June 7, 2018
ASMS 2018 described in too many words, what about this --- Amazing, dedicated, super nice and scary brilliant people everywhere who are all unified by some strange desire to use vacuum chambers and magnets and electric fields and stuff to somehow make the world a better place.
ASMS described in <140 characters?
Day 3 was awesome. My day started with Michael Shortreed describing his team's MetaMorpheus software. If you haven't used it, I strongly recommend you check it out. If you were awake at the cursed hour before 9am (whatever it's called -- I don't even know or care to find out) and got to see it, I'm sure you know why.
I have a problem (or two, I guess...) -- but the one I'm thinking of is something about a processed protein that gets stuck in something weird and I need to know how much of that protein is stuck in that weird thing (like -- up to what amino acid is it stuck in this weird thing, does that make sense? -- this is often about the level I understand around work) and the talk on DiPS presented the solution I've been looking for! You can read about it here. DiPs relies on multiply microwave assisted acid protein cleavage and de novo sequencing to fully sequence proteins. So -- if you're protein is stuck in something weird up to an unknown point, maybe you can figure out exactly where the sequence ends!! This digestion isn't new, of course, but the strategy for overlaying the fragments from different runs is EXACTLY the right twist to make this work (I think!)
Random favorite stuff:
Hong Wang's (pretty sure he's in Junmin Peng's lab) from St. Jude's -- comprehensive proteogenomic study on how to deal with rare (low n) diseases was a serious WOW. Had to text colleagues to come see it (including an infamous MD I work with, so that I could verify that it was as smart as I thought it was), but it hasn't been published yet. Can't wait to talk about it, though. Google Scholar Alert set!
Mark Chance showed CrossTalker -- it isn't out yet, either?!?! I've had the fortune of getting to spend some time with Dani Schlatzer in the phenomenal Case Western Proteomics Center. They have amazing in house tools -- and it looks like some are coming to the outside world. CrossTalker is an open network and pathway analysis tool that has some really cool twists. I hope to use it soon.
Amber Moseley (who was too flooded with interested people for me to catch up with) showed an application of thermal profiling for studying mutations!! I swear, I always think about this tool as one of those things that is amazingly powerful -- but is looking for an application. Amber's team at IUPUI found one and it's scary smart.
Pierce is releasing a TMT QC reagent!! It isn't on their site, but -- how useful will that be?
I got an inside perspective of what we'll see out of CPTAC 3 from David Clark at JHU -- just the controls they are using is worth a serious publication. This going to be an amazing dataset to mine forever. (Hurry up and get it done, y'all!!)
The middle of my day was software demos and looking at sample prep robots. Paul Stemmer just upgraded his robots at Wayne State to the Agilent AssayMap and had nothing but good things to say -- given the throughput and quality of work that comes out of that lab, that says something. However -- that robot is VERY sophisticated and that translates to pricy in robotics. I know a number of people who are loving the cheaper (though write your own python scripts to use it...) OpenTron route.
Okay -- these are clearly some of my favorite people to talk about (do other proteomics people have real life PIRATE STORIES?!?!) but Mak Saito's team at WHOI has been doing amazing stuff profiling the metaproteomics of the sea. Jacyln from that group (probably doesn't need a last name if you spell her first correctly) detailed the study of huge ocean zones where there is virtually no dissolved oxygen. Huge areas completely full of some of this planet's most ancient (pre-oxygenic catastrophe! life) and how she's studying it with proteomics. Wait on that paper -- I suspect there is a reason she's getting NASA funding, for real.
However -- they've got loads and loads of data from the ocean and they've been working to develop standards for oceanography data collection and dissemination. OceanProtein Portal is the first attempt at the dissemination part.
Check this out -- you put in a peptide sequence (partial or intact, or identifier) and you can see if they've collected information on it and it's abundance -- at different spots on their global explorations. (P.S. I've provided feedback that the word "cruise" is not a good PR decision for what are extremely long and dangerous sounding deep see mission)
This obviously isn't my field, so I can't really do anything smart with it except punch in peptides, but for people who are in metagenomics/metaproteomics how lucky are they to look at such a cool resource?!?!?
Woooooo!!!! ASMS, yo!!