Something has been missing from ion traps, according to R. Graham Cooks, a chemistry professor at Purdue University who’s been developing the devices for more than two decades. Typically these mass analyzers capture ions with various voltages and frequencies applied across their electrodes. And typically, they can do only one type of tandem mass spec (MS/MS) experiment—a two-stage experiment that improves the ability of the instrument to identify components of complex mixtures.
For instance, until recently, if scientists wanted to use an ion trap to run an MS/MS experiment, virtually the only one available was a so-called product ion scan. In this experiment, you apply a voltage to the trap to confine a particular “precursor” ion. After that precursor is fragmented, the resulting ion bits are analyzed during a second scan.
Other mass analyzers, such as the triple quadrupole, have a broader repertoire of MS/MS scans, including the precursor ion scan, which identifies all precursors that produce a particular fragment ion, and the neutral-loss scan, which looks for fragments that have lost a particular neutral functional group. People thought those scans were too complicated for ion traps.
Cooks and his team, including graduate student Dalton T. Snyder, have shown that those scans can indeed be performed on quadrupole ion traps, including miniature ones (J. Am. Soc. Mass Spectrom. 2018, DOI: 10.1007/s13361-018-1922-1).
“There is now a series of scan methods that have been described out of this lab, which parallel all the experiments you can do with a triple quad and then some others that you can’t do with a triple quad,” Cooks says.
To achieve scans such as precursor ion and neutral-loss scans, Cooks’s group doesn’t need to scan the radio-frequency voltage that’s used to trap ions. Scanning the amplitude of the RF voltage is usually the way to record mass spectra with ion traps.
For the new scans, the researchers instead keep the amplitude fixed. And they apply various excitation frequencies to the electrodes that make up the trap.
“Once you’ve got the voltage fixed, you can play ‘notes’ on the resonant frequencies of the ions, and you can excite them and eject them in different directions,” Cooks says.
The mass analyzer itself is unchanged, Snyder explains. The difference is the scientists now apply resonant frequencies to the ions in directions other than toward the detector, the scheme that’s typically used.
“People thought the orthogonal direction, where there is no detector, was useless,” Snyder says. “But you can do all sorts of things in the orthogonal dimension. You can do scans we thought were possible only on a triple quad.”