Two-dimensional tandem mass spectrometry in a linear quadrupole ion trap using consecutive product ion sweeps

Abstract

Two-dimensional tandem mass spectrometry (2D-MS/MS) is a powerful analysis technique which can quickly produce a map of all precursor-product ion relationships within a sample, from a single ion injection event, and is greatly suited to low-cost instrumentation like ion traps. The ability to record this type of information in an unsupervised and unbiased manner makes this technique highly amenable to artificial intelligence-based workflows which can statistically examine the datasets to perform structural elucidation, generate more confident peak assignments, and/or discover new chemistries. Previous implementations of the 2D-MS/MS scan function kept the RF voltage applied to the trap constant and scanned an auxiliary frequency to eject and detect the product ions. A direct consequence of this is that ions of higher precursor and product m/z would have a lower observed mass resolution and sensitivity, leading to more potential candidates for peak identification algorithms and higher uncertainty in the reported results. Herein, we describe a new approach to 2D-MS/MS analysis in a linear quadrupole ion trap which utilizes consecutive, traditional, RF amplitude ramps to resonantly eject ions from the trap near the boundary of the Mathieu stability diagram. Relative to its predecessors, the technique does require more time to acquire, however, it necessitates fewer instrument modifications and has more robust calibration procedures. More importantly though, its use produces higher sensitivity spectra with constant 2D peak resolutions (3 Da FWHM @ 125 kDa/s), which can be predicted based on the set product ion scan rate and resonant ejection point. Additional discussion is aimed at methods by which the scan might be improved, or optimized, for higher speed workflows utilizing sample arrays. This work paves the path towards isotopically resolved 2D-MS/MS spectra, which would greatly enhance the power of the technique.