TY - JOUR

T1 - Trapped Ion Mobility Spectrometry (TIMS) and Parallel Accumulation - Serial Fragmentation (PASEF) in Proteomics

AU - Meier, Florian

AU - Park, Melvin A

AU - Mann, Matthias

N1 - Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.

PY - 2021/8/17

Y1 - 2021/8/17

N2 - Recent advances in efficiency and ease of implementation have rekindled interest in ion mobility spectrometry, a technique which separates gas phase ions by their size and shape and which can be hybridized with conventional liquid chromatography and mass spectrometry. Here, we review the recent development of trapped ion mobility spectrometry (TIMS) coupled to time-of-flight 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 - time-of-flight (timsTOF) 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 ultra-sensitive measurements down to single cells. The speed and accuracy of TIMS and PASEF also enable precise measurements of collisional cross section (CCS) 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 CCS 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 post-processing to increase confidence in peptide identifications. These developments make timsTOF-PASEF a powerful and expandable platform for proteomics and beyond.

AB - Recent advances in efficiency and ease of implementation have rekindled interest in ion mobility spectrometry, a technique which separates gas phase ions by their size and shape and which can be hybridized with conventional liquid chromatography and mass spectrometry. Here, we review the recent development of trapped ion mobility spectrometry (TIMS) coupled to time-of-flight 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 - time-of-flight (timsTOF) 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 ultra-sensitive measurements down to single cells. The speed and accuracy of TIMS and PASEF also enable precise measurements of collisional cross section (CCS) 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 CCS 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 post-processing to increase confidence in peptide identifications. These developments make timsTOF-PASEF a powerful and expandable platform for proteomics and beyond.

U2 - 10.1016/j.mcpro.2021.100138

DO - 10.1016/j.mcpro.2021.100138

M3 - Journal article

C2 - 34416385

SP - 100138

JO - Molecular and Cellular Proteomics

JF - Molecular and Cellular Proteomics

SN - 1535-9476

ER -