Enabling one- and two-dimensional mass spectrometry in a linear quadrupole ion trap

Abstract

Two-dimensional tandem mass spectrometry (2D-MS/MS) provides rapid unsupervised access to all product ions of all ionized precursor ions in a single scan, and as such, is a powerful analysis method for quadrupole ion traps. However, the way in which 2D-MS/MS was previously implemented on our Thermo LTQ prevented us from switching back and forth from conventional one-dimensional mass spectrometry (1D-MS) without significant effort and on any reasonable timescale. This drawback inhibited our ability to perform standard workflows such as mass calibration and automatic voltage optimizations, but also made it impractical to perform cross-validation between modes on the same instrument. In effect, this reduced our data quality, preventing us from generating 2D-MS/MS spectral libraries with high fidelity, and from comparing spectra collected under differing conditions (user, time, etc.). In this study, an Arduino Uno microcontroller is used to control several electrical/electromechanical switches and the timing of all experimental subsystems in response to the instrument trigger output and a user selected operating mode. With a selection made, the user simply needs to adjust a few software parameters and change the bath gas of the linear ion trap. The ability to rapidly switch operational modes is demonstrated using a mixture of tetraalkylammonium cations for which spectra are collected in both 1D (helium) and 2D (nitrogen) modes in less than 1 min. By calibrating and measuring the RF amplitude control signal in 1D mode it is possible to calculate the applied RF amplitude in 2D mode, thereby allowing the user to determine relevant quadrupole operating parameters for a particular sample. Details of the system and its modifications are provided.