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Pimp my spec!
Jeffrey M. Perkel, Ph.D.
BioTechniques, Vol. 53, No. 6, December 2012, pp. 339–343
Full Text (PDF)

In the early 1990s, Michael Westphall, with his newly minted Ph.D. in experimental astrophysics, found himself in something of a career crisis. The end of the Cold War meant the start of a new era of geopolitics and a downshift in American defense spending. Unfortunately, as Westphall notes, the defense industry is “probably the main employer of physicists outside of academia.”

However, Westphall's love was not so much astrophysics as it was instrumentation — building widgets. In astrophysics, items such as cosmic ray detectors cannot simply be purchased on; they're a roll-your-own kind of gadget. “Nothing they used was off-the-shelf,” he says. “That's what drew my attention.”

With experimental astrophysics out, Westphall cast about for other options, and found an emerging area of research that needed extensive technology development and had lots of money: the Human Genome Project. He ended up at the University of Wisconsin-Madison, working with Lloyd Smith on genome technology development. Specifically, they pursued the idea of using mass spectrometers to sequence DNA.

As Westphall describes it, it isn't so far a leap from astrophysics to mass spectrometry as one might think. “It's just a little mini-particle accelerator in the lab.” The only difference, he says, is that in astrophysics, the goal is to detect energetic particles; in mass spectrometry, those particles first have to be ionized and then accelerated.

Two decades later, Westphall has migrated from genomics applications of mass spec to proteomics. He's still enamored of the mass spec technology — so much so, in fact, that he returned to the field after a short stint in rocketry in 2009, designing a far-UV polarimetry detector for a so-called “sounding rocket.” “I really missed doing mass spectrometry of all things, much to my surprise.”

That makes Westphall a member of a somewhat exclusive club, a small cadre of researchers pushing the edge of mass spectrometry technology development. That's befitting for someone whose title is “distinguished instrument innovator.” Yet, anyone can do it. All it takes is time, money, drive, and a healthy understanding of ion physics.

An Orbitrap for a GC

Westphall's mass spectrometry expertise now can be found at the University of Wisconsin in the lab of chemist and mass spec expert, Josh Coon, for whom he has worked the past three years. Coon, who co-developed one of the proteomics field's key mass spectrometric techniques, electron transfer dissociation (ETD), calls Westphall, “the lead scientist in my lab on all things instrumentation.”

At the moment, Westphall is leading an effort to develop a new component to accelerate ETD. ETD involves introducing a reactive anion into a sealed chamber along with the positively charged cations being measured. The transfer of an electron from anion to cation causes the cation (ie, a peptide) to break in predictable ways along the peptide backbone, but — and this is key — without disrupting protein modifications.

In proteomics, speed is critical, and accelerating ETD can accelerate the whole workflow. Problem is that you can't simply flip a switch to speed the reaction; you have to build some new hardware. Specifically, says Westphall, you need to design a new ion trap that is narrower than standard traps, but longer and with a higher radio frequency field strength, “so that you're really confining this ion cloud into as small a space as possible.”

While the intent of the new ETD ion trap is to be compatible, in theory, with any mass spec, other instrument enhancement projects tend to be more specific. Orbitraps are incredibly popular among biological mass spectrometrists, offering much of the resolution and mass accuracy of top-of-the-line FT-ICR mass specs at a fraction of the price. Yet they are designed to work with liquid chromatography sources, making them perfect for chromatographically separated proteins and peptides but useless for the many small molecules that can only be studied in the gas phase.

Westphall and Coon decided to rectify this limitation by creating a GC-Orbitrap. According to Westphall, the process of implementing a GC source on the instrument involved considerable hardware work — replacing the instrument's atmospheric inlet with a GC ionization source, inserting quadrupoles for ion selection, adding transfer optics to move the molecules, and so on.

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