Trapped Ion Mobility Spectrometry and Parallel Accumulation–Serial Fragmentation in Proteomics

Recent advances in efficiency and ease of implementation have rekindled interest in ion mobility spectrometry, a technique that separates gas phase ions by their size and shape and that can be hybridized with conventional LC and MS. Here, we review the recent development of trapped ion mobility spectrometry (TIMS) coupled to TOF mass analysis. In particular, the parallel accumulation–serial fragmentation (PASEF) operation mode offers unique advantages in terms of sequencing speed and sensitivity. Its defining feature is that it synchronizes the release of ions from the TIMS device with the downstream selection of precursors for fragmentation in a TIMS quadrupole TOF configuration. As ions are compressed into narrow ion mobility peaks, the number of peptide fragment ion spectra obtained in data-dependent or targeted analyses can be increased by an order of magnitude without compromising sensitivity. Taking advantage of the correlation between ion mobility and mass, the PASEF principle also multiplies the efficiency of data-independent acquisition. This makes the technology well suited for rapid proteome profiling, an increasingly important attribute in clinical proteomics, as well as for ultrasensitive measurements down to single cells. The speed and accuracy of TIMS and PASEF also enable precise measurements of collisional cross section values at the scale of more than a million data points and the development of neural networks capable of predicting them based only on peptide sequences. Peptide collisional cross section values can differ for isobaric sequences or positional isomers of post-translational modifications. This additional information may be leveraged in real time to direct data acquisition or in postprocessing to increase confidence in peptide identifications. These developments make TIMS quadrupole TOF PASEF a powerful and expandable platform for proteomics and beyond.
Graphical Abstract
Highlights • TIMS is a compact, highly efficient, and flexible ion mobility device. • PASEF increases sequencing speed without compromising sensitivity. • Collisional cross-section information remains to be fully explored and utilized.
In Brief The combination of ion mobility and MS is increasingly attractive in the field of proteomics research. Here, we provide a perspective on the recent development of TIMS and PASEF. TIMS offers an additional dimension of separation and collisional cross-section information, whereas PASEF greatly increases the efficiency of MS/MS experiments. As the user base broadens and computational tools evolve, a wide range of applications emerge from structural to single-cell proteomics.