to BioTechniques free email alert service to receive content updates.
Pimp my spec!
Jeffrey M. Perkel, Ph.D.
Full Text (PDF)

After graduation, Compton rejoined Kelleher, now at Northwestern University. There, he was charged with building what Kelleher calls “a big waiting room” — a roomier octopole ion trap — on the FT-ICR affectionately known as “Earl.” (The name is a reference to Earl Grey tea, as the machine comes from Britain. Other lab instruments, though, are named after one-word movie titles or TV shows, explains Kelleher. Thus, the lab has spent millions on mass specs christened Avatar (complete with Jake Sully action figure), Inception, Blade, Moonraker, Quicksilver, and Tron.)

Compton's new ion trap is called a “Bruce-o-pole,” in honor of Bruce Wilcox, a researcher at the National High Magnetic Field Laboratory at Florida State University, who first implemented the idea. The device is designed to catch a large number of ions in either a pulsed or continuous fashion and then dump them into the ICR cell in a single load.

Adding ion optics, vacuum devices, and a longer ion path, all to optimize performance and add fragmentation options, Compton was able to improve upon Wilcox's original design. “Unfortunately, doing that winds you up with seven additional optics with eight additional voltages,” he says. “So, life starts getting pretty complicated pretty quick.” He also added f-ETD and an additional resolving quadrupole for ion selection — all of which has to be tuned just so in ITCL.

In total, Compton spent two years getting Earl (and the rest of Northwestern's Proteomics Center of Excellence) up to speed. Yet, from the users’ perspective, the machine is no more complicated; all they see are a few new options in the instrument control software — one for selecting and configuring the method of fragmentation, the other to select how many fill steps to use before initiating the ICR run.

“One of my goals and one of my requirements when I design or do a modification,” says Compton, “is that it has be something that I don't have to support once it's done.”

Ready to tinker yourself?

Anybody with the interest, along a good working knowledge of ion motion, can muck with a mass spectrometer. But that doesn't mean they should.

Senko says commercial systems are often so complex that even in-house people at Thermo can have problems. “There's just so many things that can go wrong when you attempt to modify it that it's quite remarkable that anybody is ever successful,” he says.

In part, that's because a mass spec isn't like a computer, where the parts are pretested and conform to some standard. A quadrupole from Thermo will use different materials, and have different dimensions, than a similar quad from Bruker Daltonics or Agilent Technologies.

“These are really like finely tuned race cars, and the average person should not be jumping in there under the hood trying to make it better,” says Jennifer Brodbelt, the William H. Wade Endowed Professor of Chemistry at the University of Texas, Austin.

Brodbelt has spent 20-odd years tweaking mass specs in her lab, developing photodissociation methods using lasers to fragment ions instead of collisions or chemical reactions. She recently co-authored a paper in which an Orbitrap Elite mass spec equipped with ultraviolet photodissociation (UVPD) was used to study tyrosine sulfation in bacteria, a modification that is too fragile to be studied using conventional fragmentation strategies.

Brodbelt says the main skill required to work on mass specs in her lab is a desire to work with ones’ hands. “Nothing extreme, but someone who's not afraid to pick up a tool…a tinkerer.” In the case of the UVPD Orbitrap the job was fairly easy — in fact, it was working within two days — but was facilitated by Thermo, as mass specs don't normally contain ports for adding an optical window for the laser beam.

University of Washington mass spectrometrist James Bruce, who is building a 10-cell FT-ICR array from scratch to enable simultaneous high-resolution analysis of unfractionated peptide fragments across a wide mass range, says mass spec tinkers require a diverse set of skills. A key hire for him was a cyclotron physicist with expertise in vacuum technology and ion sources. Successful tinkerers, says Bruce, “really need to know something about ion physics. They need to know something about how to make ion lenses and how to guide ions, how to trap ions in the gas phase.”

  1    2    3    4