Wednesday, June 6, 2018

ASMS2018 -- Ben's even more useless recap of Day 2

Hey! Are you looking for a postdoc who can make great proteomics informatics posters? Is quality of handwriting not the highest priority? 😋  You can reach Donxue (she's in Kuster's lab! I hear they're pretty good there.) here.

With that out of the way (clever idea, Dx!) time to dig out the ASMS 2018 day 2 notes. Besides crack 20,000 steps again today...umm...what did I do again? 

Wow -- Ben Garcia's acceptance speech of the Biemann Medal -- wow -- informative, funny, sincere

--- included a very detailed SpiderMan reference (there is a histone thingy on that chalk board in the movie)-- what more could you ask for? Seriously... one of the best talks I've EVER seen about anything.  I still don't quite understand what a histone is or does, but it is clearly a problem that nothing currently exists that is better suited to conquer this problem than our technologies.

This was PROTEOGENOMICS day! How do we finally merge all this transcriptomics and proteomics data together? And there are crazy powerful tools out and more coming.

Some highlights!

PepQuery is live here and can build off of VCF, BED GTF or WTF files (one of those is made up, the rest are things your genetics people talk about -- and is peptide centric comparisons off of those file types.

On that same tilt -- ProteomeGenerator is also on BiorXIV here. More tools to make integrating all this data together, please!

Side note --
RawMeat may be coming back finally! Should be investigated. You might LOL when you find out what it's called (pdf download of poster is here)

Something ABSOLUTELY WORTH CHECKING OUT -- PeakStrainer --> it reads directly from RAW and does some amazing stuff in terms of discerning peptides from noise based -- not on intensity -- but on the frequency. Super smart....

Back to the proteogenomics -- besides the tools there were amazing examples of large integrations from tumor samples to patient cohorts to using the two to tell between human and mouse in xenograft models. With better tools maybe all of this is going to become easier (it still seems tough and scary to me...but there are some great templates coming)

Just to double back to the very top -- Donxue's poster was on healthy tissues, something I feel like we sometimes forget about the need for profiling. If she did that work (it doesn't appear to be out yet) and you've got a position somewhere on earth that isn't too cold, it would be my recommendation you shoot her an email -- if only to learn about what she's working on. Suuuper cool.

Okay --coffee -- more informatics --go!!

1 comment:

  1. Just an FYI, along with some other tools like the Fusion API, the XCalibur workbench can be followed on the Thermo GitHub page: