Friday, January 13, 2017

Cell-specific proteomics for biological discovery!

I know my Twitter feed keeps telling me I should be boycotting Elsevier for something or other, but if I had I'd missed this stellar new (and open access!) review from Shannon Stone et al.,.

Half-way through this I had some serious questions regarding the background of this lab. I mean this in a very positive way!  It is clear from the offset that this isn't coming from either a classically trained genomics or proteomics lab. Dr. Tirrell was originally a polymer chemist and engineer, but his lab is applying these approaches to biological systems. I suspect we're going to hear a lot from them, because what they are doing is not only unique (to my knowledge!), but it also seems seriously brilliant.

While researching "who the heck are these people?" I ran across this paper from last year and it deserves more time than I have here (they induce a mutation so they can chemically tag proteins from just their organism with the mutation!).

If you say to me cell-specific proteomics -- I'm immediately going to immediately think you are talking about flow cytometry or laser capture microdissection. How else are you going to separate distinct cell type populations for proteomics?

This is NOT, however what this group is focusing on! They are using chemical labeling strategies that will allow them to either physically separate the cells OR to just be able to tell afterward from the proteomics or transcriptomics where that particular cell came from!

This paper is OPEN, so I'm gonna borrow part of a table to show you why you should check this out!

(Hopefully the reason I'm not supposed to be reading Elsevier isn't because they've been suing bloggers for posting parts of tables....if it is, someone please let me know!)

This is the center piece of this awesome paper. The method -- what you can study -- a brief overview -- the two "Yes" is whether it is compatible with secreted proteins then whether it is compatible with PTMs. They then go into advantages/disadvantages of the techniques!

Each one of these method bears further investigation!

Why? Oh -- because sometimes you just can't separate the individual cells. And -- this is the real advantage in my mind -- maybe because I've got a beautiful set of runs of mixed peptides from primates and Alveolata on my desktop and I'd give my right arm to know which peptide came from which organism -- if we had cell-specific labeling protein labeling techniques that we commonly used, can you imagine the reduction in protein inference problems?!?!  It would be staggering. Just the data reduction alone at the end -- not to mention -- the possibility of using the instrument to only focus on the tagged proteins -- but I'm getting just a little ahead of myself.

It is worth nothing that most/all of these methods seem to be for cells that are actively growing and dividing.

Summing it up -- this paper is seriously worth a read -- at the very least check out the complete table!


  1. Unfortunatley they are charging me $27.95 if I want to read it :(

  2. Thank you for the nice write-up! It's unfortunately only open access for two months by clicking the "sharing" link that I'm allowed to publish on my social media. Here's a link to that tweet:

    Please let me know if you have any questions about the review. It was a lot of fun to write because I have some amazing coauthors.

    Time to check out the rest of your blog!


    1. Thanks for the additional info, Shannon! And for the nice review!