Trapped ion mobility spectrometry (TIMS) and parallel accumulation - serial fragmentation (PASEF) enable in-depth lipidomics from minimal sample amounts

Abstract

Lipids form a highly diverse group of biomolecules fulfilling central biological functions, ranging from structural components to intercellular signaling. Yet, a comprehensive characterization of the lipidome from limited starting material, for example in tissue biopsies, remains very challenging.Here, we develop a high-sensitivity lipidomics workflow based on nanoflow liquid chromatography and trapped ion mobility spectrometry. Taking advantage of the PASEF principle (Meier et al., PMID: 26538118), we fragmented on average nine precursors in each 100 ms TIMS scans, while maintaining the full mobility resolution of co-eluting isomers. The very high acquisition speed of about 100 Hz allowed us to obtain MS/MS spectra of the vast majority of detected isotope patterns for automated lipid identification. Analyzing 1 uL of human plasma, PASEF almost doubled the number of identified lipids over standard TIMS-MS/MS and allowed us to reduce the analysis time by a factor of three without loss of coverage. Our single-extraction workflow surpasses the plasma lipid coverage of extensive multi-step protocols in common lipid classes and achieves attomole sensitivity. Building on the high precision and accuracy of TIMS collisional cross section measurements (median CV 0.2%), we compiled 1,327 lipid CCS values from human plasma, mouse liver and human cancer cells. Our study establishes PASEF in lipid analysis and paves the way for sensitive, ion mobility-enhanced lipidomics in four dimensions.

Proteogenomic analysis of granulocyte macrophage colony- stimulating factor autoantibodies in the blood of a patient with autoimmune pulmonary alveolar proteinosis

“…To date, a number of studies involving proteomic analysis of antibody structure have used an Orbitrap device that traps ions in electrostatic fields and converts them to a mass spectrum using a Fourier transform of the frequency signal 18 . In contrast, this study used a novel instrument that combines LC/MS/MS with trapped ion mobility spectrometry, which offers additional separation power and increased peak capacity over instruments that do not perform trapped ion mobility separation 14,16 . There is little information available regarding comparison in performance between Orbitrap devices and TIMS-TOF instrument.…”

A simple tool extends TIMSTOF compatibility with historic data processing tools and enables ion mobility-enhanced spectral libraries

“…As reported by others, the 1/k0 values obtained by the TIMSTOF instruments can be both reliable and predictable for each peptide, as demonstrated by the use of deep learning models. (Meier et al, 2020;Ogata and Ishihama, 2020;Vasilopoulou et al, 2019) As such, the recorded 1/k0 value for each peptide can be used as an additional confidence metric for assigning a peptide identification. Figure 3 is an example peptide spectral match with low fragment sequence confidence and a corresponding 1/k0 measurement that is > 0.073 units off of the library spectra value.…”

MS-DIAL 4: accelerating lipidomics using an MS/MS, CCS, and retention time atlas

“…2f, Supplementary Figs. 8 and 9) 14 . Notably, MS-DIAL 4 is the first vendor-free metabolomics and lipidomics software able to handle Bruker IM-DDA and Agilent-and Waters IM data-independent acquisition (DIA) with the support of IM chromatogram deconvolution.…”