2 hours in and complete brain overload here at HUPO! So much good science out there in the field!
One important side note that I think you guys will like, though. The first free OpenMS nodes for Proteome Discoverer 2.0 are now available for download. The first is LFQ for label free quan! The second is a workflow in OpenMS I'm unfamiliar with, but will read up on ASAP.
About a year ago a paper came out that introduced me to the concept of Thermal Proteome Profiling. While this concept will likely have several different applications, it is definitely really good at figuring out what proteins a drug is interacting!
Being a Nature Protocols paper, the methodology is set out completely so that any of us can go right out and replicate it. This team also developed software for Python and R that can be used to process the data and they make this all available.
Are you stuck on what that stupid drug's mechanism of action is? You should probably check out this paper!
Now, I know I've rambled on about NeuCode in this blog a bunch, but if you are unfamiliar there is a good description in this GenomeWeb article here. In a nutshell, its very much like SILAC except by NEUtron endCODE(ing) the mass discrepancies between the various channels are very very small. You are limited by the number of channels you can use by the maximum resolution of your instrument. More resolution = more NeuCode channels.
(I stole the figure above from this open access paper here.) P.S., the technology has been progressing significantly since the original study. I saw a slide a while back that suggested 40-plex is theoretically possible.
In this study, the nematodes are studied with an Orbitrap Elite that is running 480,000 resolution at the MS1 and 30k resolution at the MS/MS (which they refer to as "medium" resolution! man, I love this field!!!)
Now, you might think 480,000 resolution? That's so slow, they'll never identify anything that way! What did they see? The top 50 most abundant proteins? Well, they did a little better than that. This might be the single most extensive proteome of the nemotode out there. Along the way they did phosphoproteomics and also worked out some of the key regulators or stress response in this important model organism.
If you are still using the FACE technique or a series of different enrichment strategies leading up to FACE you might want to take a step back and think about what you want to get out of your samples. Is a generic anti-phosphotyrosine antibody still the best for what you want out of your analysis? If you are interested in pathways, for example, that preferentially use phospho-Ser, maybe there is a better option now than we had 5 years ago!
If you are looking for information on top down proteomics via Prosight or info on the Prosight nodes for Proteome Discoverer, you need to check out Proteinaceous.net.
Here is a direct link in case you have as much trouble spelling it right as I did...
Shoutout to David Kusel for the link for this one! Is there anything about the history of mass spectrometry that you've ever wanted to know? This Nature Milestones project probably has it covered. This was compiled by a huge list of authors who all seem to know at least a little about this field and is written to be accessible to everyone. It would make a great reference for our customers or collaborators who aren't really sure what magic we're doing in our noisy rooms!
This new paper in press from Yang Yu et al., at MCP is fascinating for a ton of reasons. First one, I have never heard of Wilson's disease and I had to read up on it in this Wikipedia article. In a nutshell, its a recessive genetic disease. If you get stuck with two of the copies because your traitless parents both had it then you accumulate excessive copper in your system. This copper messes with your liver and maybe your brain and it is somewhat subtle and very difficult to diagnose. Sometimes you have oddness in your eyes that is indicative, as shown above.
Another reason this is fascinating? They detail a painstaking method of directly analyzing DNA damage via LC-MS. The introduction of stable isotopes leads to an absolute quantification method via triple quad and ion trap mass spec. It is really a fascinating method because when we think DNA damage, we think about assessing downstream effects (got the right affect/effect this time, I think!). If I want to quantify DNA damage, I'm going with phospho-H2AX quantification or something like that. These guys cut out all the middlemen and go right to the DNA!
I'll not pretend to be a metabolomics expert, but its super interesting, right? In terms of sample prep, they have it far far worse than we do. At least we know how to get most proteins in one process. Metabolites? That's a different story.
Biocrates is a company that hopes to make MS based metabolomics easy. They produce QC'ed kits that are specifically focused on clinically interesting metabolites. You get the sample prep kit, the conditions for the experiment and the software to process the data. What you need is the mass spec -- and you are doing full out metabolomics!
Currently they kits are optimized for triple-quads but they are in the process of getting these powerful tools validated for the Q Exactives!
Due to some changes in what I do during the day I now get to spend a whole lot more time in the same state where my house and my dog live. In my exploration of the area for fun things to do, I lucked into a last minute chance to go to the D.C.-Baltimore mass spec club!
I learned a bunch of stuff! I got to meet a senior scientist at AP-MALDI and I think I'm going to get the chance to set up a source and do some imaging mass spec on a Q Exactive!!!
If you're around the area anywhere you should come and check this fun group out. I can't imagine missing another one of the meetings!
If you are going to beautiful Vancouver for International HUPO, you might want to pop by the Proteome Discoverer workshop where you'll get to see the introduction of this guy!
Wait? What? We just started using PD 2.0...are you crazy? Yes, but that's beside the point. PD 2.1 is a follow-up package that looks just like PD 2.0 but better. There were features and improvements that were recommended by all you users out there that just couldn't make the 2.0 cut. Its so good that I pretty much just use PD 2.1 for everything.
Here are the details!! This is meant to be interactive, not "DEATH BY POWERPOINT". Bring questions, data, whatever. This is great software and we want you to walk out of there with the ability to generate better data!
Here are the details I have right now. I'll add more info as I get it.
