Prime XS -- Advance proteomics...and the rest of science

This is SO smart.  And we need an equivalent here in the U.S.  If you want to start it, I volunteer to head it.

Prime-XS is a program ran by the EU.  It ensures 2 things:  1) That proteomics is used for scientific studies of extreme merit.  and 2) That labs participating in XS are exposed to high quality, high impact biological problems.  It is a win-win.  Top notch labs get top notch collaborators and the EU pays for it!

How it works:  Researchers in the EU countries can apply for days of access to proteomics facilities that the EU has reserved for this program.  This is how it is currently divided:

Ummm.... 621 days are available in Utrecht?  That couldn't be the Heck lab, right?  Pretty sure it is!

What a win for everybody!  How many top notch proteomics facilities can you think of that have trouble finding high impact biological questions?  Tons, right?  Let's face it.  Cool problems don't always come from the same places where our best proteomics facilities are.  This fixes it.  In one fell swoop.  Top biological problems -- top proteomics capabilities -- and we all win.

The downside is that this program is going to push the power balance in impact factor toward Europe.  Meaning we need something like this over here.

You can read more about Prime-XS here.

READ MORE - Prime XS -- Advance proteomics...and the rest of science

Rough week around here

Last thing you want to see on your primary processing PC?  3600 sector errors.  Needless to say, it is slowing things down around here.

READ MORE - Rough week around here

Fill a library with what I don't know about in shotgun proteomics

Today I got a super interesting question about Percolator and Spectral libraries.  While investigating, I figured I'd better go to the Percolator Google Group and see (btw, I think this is going to be very interesting to everybody!!!)

Anywho, while searching, I came across a whole lot of names I recognize who belong to a Crux-users Google group.  What the heck is Crux?  Umm....maybe an incredibly awesome and apparently free software package for proteomics?

On further investigation, I found Scholar references back to 2008(?!?!?!).  I feel less out of touch because it appears to be buried within the 1,000 programs and features that make up the Trans Proteomic Pipeline.

You can find out more about Crux here.  Feel free to tell me about it.  Back to Percolator....

READ MORE - Fill a library with what I don't know about in shotgun proteomics

Perform imaging analysis on a Q Exactive?!?!?!

Guess what I did this week!  Wait...I guess if you read the subject line you have an idea....

I got to hang out all week with the very nice team of scientists at Protea Biosciences in the beautiful mountains of West Virginia.  Not heard of Protea?  Me neither!  But I expect that they will rapidly be something that we'll be talking about, in part, because of this thing:

Despite it's appearance it is not, in fact, a refrigerator/toaster oven combo.  I got to play with a beta model that was open so I could see exactly what it was doing at all times.

Yes.  That is attached to a Q Exactive!  And that light inside is for the camera that directs the LASER.  I'm not going to lie and say I'm some laser ionization expert.  I'm not.  But I've spent some time on a MALDI-Orbi XL and a Rich Helm's MALDIs, but I got a crash course in it this week, and this was the most badass one I've seen.  The source is a LAESI and you can read about it at wikipedia here.  The team here has this source running on all sorts of samples.  I was just there to see if we could fine tune the Q Exactive to get even better data.  It was cool because we could get about 3 second laser pulses on our controls.  The trick was optimizing cycle time in the Q Exactive so that we could optimize every single millisecond.

Definitely a different way of thinking.  But if you think about the Q Exactive, and assume that this source can ionize virtually anything and consider those implications.  On the QE we can run, at maximum, about 13Hz. If we multiplex, this gives us a chance to monitor as many about 65 compounds per second via targeted SIM or targeted MS2 (PRM; btw, I'm considering practicality.  We can multiplex 10 compounds in the QE, but 5 is easy.  10 is trickier).  If we're just going for detection, the LAESI-QE compound can probably SIM or PRM about 150 molecules per 3 second laser pulse (we were optimizing with small molecule drug mixtures!)

What else did we do?  We worked most of yesterday optimizing native protein and top-down.  Cause the LAESI can zap native proteins right out of tissue, right off a slide, right from where you want it from.  Point to the area on the microscope and ZAP (it didn't actually make a noise...) native protein MS!  We were even able to get nice top down data on our intact native protein using the LAESI by using multiplexing on the QE to fragment multiple charge states from the isotopic envelope.  Did I mention that my week was really cool?

Anyway, this source can be put onto just about anything but, honestly, what is cooler than having imaging capabilities on the world's favorite mass spec?

BTW, imaging isn't all this lab does.  They have a really exceptional team of mass spectrometrists with experts in virtually anything you can think of from molecule elucidation through quantitative proteomics and everything in between.  (Can you tell I was  impressed this week?)

TL/DR:  You probably know about this already, I didn't, but check out Protea here!

READ MORE - Perform imaging analysis on a Q Exactive?!?!?!

Biomath calculator App

What is more annoying than doing that calculation above me?  Seriously!  I have x amount of protein in ug what is my molar concentration?  You are probably smarter than me, but I have a tendency to lose a decimal place or two.  This week I said "wow, there should be an app for that".  And there is.  Of course.

Promega has a free BioMath calculator that will do this one for you, among other things.  (Lots of DNA calculations and dilutions, but this is what I downloaded it for!)  It is available for both Android and Apple.

You can read more about it here.  A big thanks to the talented team at Protea for pointing this one out to me!

READ MORE - Biomath calculator App

I've seriously considered this.

A friend forwarded me this picture.  I'm not the only person that loves this field!!!

Then I got this one forwarded to me as well (thanks Da Jules):

READ MORE - I've seriously considered this.

Cool targeted peptide quan article in The Scientist

I had to go to the doctor today for routine checkup stuff and what magazine was at the top of the stack? This month's issue of The Scientist!  That's just how Baltimore is.  There is probably almost as many scientists here as drug addicts.  My physician is probably married to a researcher at Hopkins or UMD or something.

Anyway, there is a great article this month describing how to move from discovery to targeted proteomics, as well as a description of each open source platform.  This'll come to no surprise if you've used it at all, but Skyline made the top of their list.

A couple of these platforms were new to me and it might be worth it to check out this nice little review.  Or even to forward it to collaborators.  It is concise and nicely written.  You can find it here.

READ MORE - Cool targeted peptide quan article in The Scientist