Weighing the World: Why Mass Spectrometry is Changing How We Do Everything

WOOOOHHHOOOOOO!!!!!

This has been a big month for me.  Another project is successfully off my desk and I don't have to think about it anymore!

My new book:  Weighing the World:  Why Mass Spec is Changing How We Do Everything was just launched on Amazon.  Currently, only the paperback is available, but the Kindle versions will be up soon (only for color Kindle readers, unfortunately, I think...I have to read more of these emails...) and it will also be distributed by Barnes and Noble (possibly also available via Nook, though I'm not 100% on that one....)

The book isn't really for you guys (my audience of expert mass spectrometrists!).  It is intended for people outside of the field.  Its a pop-sci look at where mass specs are right now, an overview of how they work, and a short summary of loads of different types of research that we do on them.  As such, I kept it pretty simple (heck, I don't even talk about isotopes until one of the last chapters)

I picked a lot of my favorite papers from the last 5 years or so and talked about:
The mass spec on Curiosity
Forensic applications
Atomic mass spec
Phosphoproteomics of the brain
Drug discovery
Proteoisoforms
How the railroads are using mass specs

I started this project almost 3 years ago and was pretty tired of looking at it, lol!

I'm not super-psyched about the Amazon front page for it, but you can check it out here if you want.

READ MORE - Weighing the World: Why Mass Spectrometry is Changing How We Do Everything

Normalized collision energy calculation for Q Exactive

I get this question all the time.  And I got the answer when I was in Bremen 2 summers ago, and always mean to put it up here:

Q:  What is the formula the Q Exactive uses for normalizing the collision energy?  Or how do we go from a NCE setting to the actual electron volts used for each fragmentation?

I'm going to give you the equation and explain it as I understand it (I'm a biologist, so chill out):

The formula:

Absolute energy (eV) = (settling NCE) x (Isolation center) / (500 m/z) x (charge factor)

Charge factors are as so:
Charge/charge factor
2/0.9
3/0.85
4/0.8
5/0.75
>5/0.75

So.... if you set the QE to do a NCE of 40 and you hit a 1,000 m/z ion with a charge state of 1
(40) x (1,000)/500 x 1 = 80 eV

Now, this was the equation for the original QE and good for the software version that was out 2 summers ago (August,2012).  I can't speak to how this equation has been adjusted or changed for new software versions or for the QE Plus, but it at least gives you a good idea, right?

READ MORE - Normalized collision energy calculation for Q Exactive

SpectroNaut: Hyper Reaction Monitoring

I keep forgetting about this one.  Biognosys is a new company that is pushing "next generation" quantitative mass spectrometry.  They have a cool idea.  Free, mutli-vendor software for label free analysis, particularly SWATH and DIA.  Why not just use Skyline?  Cause Biognosys has figured out how to do QC during this experiment.  You buy the QC standards from these guys and they use these standards to make adjustments to your data.  Cool idea and a really cool website design.

READ MORE - SpectroNaut: Hyper Reaction Monitoring

Are you an awesome scientist? Want the coolest job ever?

WOOOOHHHHOOOO!!!!

My day job is recruiting an associate application scientist.  I'll put the job listings below.

Requirements (my list... official list below):
1) You're awesome
2) You can do LC-MS.  You don't have to be the best in the world...yet...you'll get trained to be!
3) You don't mind hanging out with cool scientists all over the continent (and sometimes the globe)
4) You are good at problem solving

Interested?  Email me at:  orsburn@vt.edu (my reference might be useful)

Official listings!

Associate Application Scientist

A dynamic and self-motivating individual is required to support state-of-the-art LCMS instrumentation as an Associate Application Scientist. As a member of the Thermo Fisher Scientific North America Field Applications Team, the candidate will work within a multi-disciplinary matrix team that includes regional sales representatives, marketing and service professionals, product development scientists, and engineers.  Primary responsibilities will be to aid and help customers become more successful with their LCMS Instrumentation related to protein applications.  Additional responsibilities include technical support for the demonstration labs and creation of customer facing educational materials.

Essential Duties and Responsibilities

         Provide technical and application assistance in response to customer enquiries, including education, training and on-site visits.

         Work with Senior Application Scientist to define meaningful triage process for customers

         Provide routine maintenance on Mass Spectrometry equipment as appropriate

         Miscellaneous duties as assigned.

Required Education and Experience:

         BS. in Chemistry or a Bioscience or equivalent.

         1+ years of hands on LCMS experience with protein LCMS workflows and associated informatics is required.

         Experience with Orbitrap instrumentation and Liquid Chromatography is highly desirable

         Requires Good English and excellent communication skills, both verbal and written.

         Good project and time management skills required.

         Must be willing and able to travel (up to 50%).

Desired Education and Experience:

         BS education in science.

         Previous experience on Thermo Scientific MS instrumentation preferred but not essential.

Knowledge, Skills, and Abilities necessary to perform essential functions

         Knowledge of basic chemistry principles.

         Knowledge of liquid chromatography and Mass Spectrometry principles and instruments.

         Experience with Microsoft’s basic software (Word, Excel, PowerPoint). 

         Ability to present experimental results and have good verbal and written communication skills.

         Possess analytical and problem solving skills.

READ MORE - Are you an awesome scientist? Want the coolest job ever?

Human proteome maps part 2: Digging deeper into ProteomicsDB

Wow.  The readers have spoken.  In 6 short days, my comparison of the 2 human proteome maps is already my 3rd most popular post of all time.  You can read part 1 here.

Yeah, cause I totally needed more reasons to explore these huge releases in my field!  What better thing to do on a long train ride this early morning?  For now, I think I've shown you all that the Human Proteome Map.org can do, but we've really only scratched the surface of what resources are available from ProteomicsDB.

To start off, I'm going to Browse Proteins.  And I'm not letting the Kuster lab off easy this time.  Let's see how they do with Integrin Alpha 5 (one of my favorite proteins and a nasty one to work with via mass spec. Membrane....ewww...)

First off.  It found it!  As well as isoforms.  Man, I love this thing....  I'm going to stick to full length isoform 1.  This is the summary page.

The chromosome it's on!  All the IDs!  Graphical maps of the peptide coverage, GO and links.  I'm a little confused by the illustration...probably a place the Kuster lab was slacking.  Guess I'll click on it just in case...

...oh...its DOMAIN MATCH maps!?!?  With confidence statistics.  This is via a page called SMART:  the Simple Modular Architecture Research Tool.  Something to investigate later. Next tab:

Okay!  Finally something that us normal human beings can do.  Assemble a sequence coverage map.  Did I mention that this protein sucks to work with?  From this map, you might not believe me though...

Next tab!  Whats a protease map?

Definitely click on this one to expand it.  It theoretically digests your peptide.  Big deal, the Protein Prospector has been able to do that for 20 years.  The metrics are pretty cool, though.  You pick the enzyme you want from the ones available (user customizable enzyme might be nice; minor suggestion) and it does the digest.  Hover over the map and the sequence appears in a little bubble.  The mouse obscures it a little, but it's there.  The cool thing is the % theoretical in the lower right hand.  I was pretty psyched the other day about manually calculated % theoretical coverage, and this thing does it automatically (so does X!Tandem, I'm told).  Nice to have all these features in one place!

Next tab.  Proteotypicity?

I choose iTRAQ and hit the calculate button:

...and I get spectral libraries for iTRAQ labeled peptides from the protein.  Terminology is weird/confusing, but the data is incredibly thorough (see the cool black line at the front where the reporter ions are?)

In part 1, I showed you the expression maps. Let's skip to the Projects tab:

Nice cropping job...did I mention I'm on a train?  Anyway, this is another cool tab.  For example, Mendoza_JPR_2013 found 17 unique peptides from ITGA5.  If I want 15 peptides, I can click the PubMed link, go to the Mendoza paper, and use the method they used (its a membrane paper, btw).  I can follow the Project link and actually download all the RAW data files for that project.

I'm going to cut this short now.  The WiFi speed on this train has dropped dramatically and uploading these images has become a pain.  I hope that this give you some sense of the insane amount of work they have put into this resource for us.

READ MORE - Human proteome maps part 2: Digging deeper into ProteomicsDB

PepExplorer -- multi-engine solution for de novo

What is the biggest problem with de novo peptide sequencing?  I think the consensus is definitely false discoveries.  There are some clever solutions out there.  PEAKS, in specific, has worked very hard over the last several years to develop and improve their FDR calculations, and to make those mechanisms public.

This new paper (currently in press at MCP, so open access) from Leprevost et. al., has taken a good hard swing at this problem and I really like their approach.

This paper introduces us to PepExplorer, a new algorithm that can compile the results of different de novo engines and compare them to help us get a feel for the confidence of our findings.  For example, if PepNovo+ and PEAKS (which are completely different algorithms) both give you high scores for a sequence identity (and, even better, it makes it through PEAKS FDR!) then we can be a lot more confident about that result.

I like the approach, but I can't speak to the software yet.  I'm pretty busy leading up to this ASMS thing.  If you happen to check it out, please post your opinions in the comments section.  Hopefully I'll get around to putting up my impressions later in the summer.

You can download PepExplorer here.

READ MORE - PepExplorer -- multi-engine solution for de novo

Scientific Data -- an awesome new journal!

Maybe y'all already know about this one, but it was new to me!

Nature has started a new journal that is solely for the description of cool data sets.  You know that experiment that didn't work?  The one where you ran the Orbi Velos for 3 months and didn't come up with a biomarker in those cell lines?

We need to do something with that data set!  Maybe that biomarker is a PTM nobody knew about!  If not, maybe just having it out there would stop me from trying that same experiment!  Better yet, maybe your n just wasn't big enough to successfully pull out the interesting stuff.  Maybe combining your "bad" data set with my "bad" data set would give us a big enough sample to get something really cool.

This journal is a BIG step in the right direction.  Lets get all this data out there!  And it's open source!

Another great one?

Hell yes!  I don't want to waste all my time doing experiments that you know don't work!  The impact factor is 1.1?  Who cares!  You publishing your stuff that doesn't work keeps other people from wasting their time.  And if somebody had published that experiment first then neither of you would have wasted your time!  We move forward.  Science moves forward.

READ MORE - Scientific Data -- an awesome new journal!