Comparison of Data-Dependent Acquisition, Data-Independent Acquisition, and Parallel Reaction Monitoring in Trapped Ion Mobility Spectrometry–Time-of-Flight Tandem Mass Spectrometry-Based Lipidomics

Comparison of Data-Dependent Acquisition, Data-Independent Acquisition, and Parallel Reaction Monitoring in Trapped Ion Mobility Spectrometry–Time-of-Flight Tandem Mass Spectrometry-Based Lipidomics

The parallel accumulation–serial fragmentation (PASEF) approach based on trapped ion mobility spectrometry (TIMS) enables mobility-resolved fragmentation and a higher number of fragments in the same time period compared to conventional MS/MS experiments. Furthermore, the ion mobility dimension offer...

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Bibliographic Details
Published in:Analytical chemistry (Washington) Vol. 95; no. 25; pp. 9488 - 9496
Main Authors: Rudt, E., Feldhaus, M., Margraf, C. G., Schlehuber, S., Schubert, A., Heuckeroth, S., Karst, U., Jeck, V., Meyer, S. W., Korf, A., Hayen, H.
Format: Journal Article
Language:English
Published: United States American Chemical Society 27-06-2023
Subjects:
Blood plasma
Chemistry
Chromatography, Liquid - methods
Data Accuracy
Fragmentation
Fragments
Humans
Ion Mobility Spectrometry
Ionic mobility
Ions
Lipidomics - methods
Lipids
Liquid chromatography
Mass spectrometry
Mass spectroscopy
Mobility
Monitoring
Phospholipids
Precursors
Proteomics
Retention time
Scientific imaging
Sensitivity
Spectra
Tandem Mass Spectrometry - methods
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Summary:The parallel accumulation–serial fragmentation (PASEF) approach based on trapped ion mobility spectrometry (TIMS) enables mobility-resolved fragmentation and a higher number of fragments in the same time period compared to conventional MS/MS experiments. Furthermore, the ion mobility dimension offers novel approaches for fragmentation. Using parallel reaction monitoring (prm), the ion mobility dimension allows a more accurate selection of precursor windows, while using data-independent aquisition (dia) spectral quality is improved through ion-mobility filtering. Owing to favorable implementation in proteomics, the transferability of these PASEF modes to lipidomics is of great interest, especially as a result of the high complexity of analytes with similar fragments. However, these novel PASEF modes have not yet been thoroughly evaluated for lipidomics applications. Therefore, data-dependent acquisition (dda)-, dia-, and prm-PASEF were compared using hydrophilic interaction liquid chromatography (HILIC) for phospholipid class separation in human plasma samples. Results show that all three PASEF modes are generally suitable for usage in lipidomics. Although dia-PASEF achieves a high sensitivity in generating MS/MS spectra, the fragment-to-precursor assignment for lipids with both, similar retention time as well as ion mobility, was difficult in HILIC-MS/MS. Therefore, dda-PASEF is the method of choice to investigate unknown samples. However, the best data quality was achieved by prm-PASEF, owing to the focus on fragmentation of specified targets. The high selectivity and sensitivity in generating MS/MS spectra of prm-PASEF could be a potential alternative for targeted lipidomics, e.g., in clinical applications.
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content type line 23
ISSN:0003-2700
1520-6882
DOI:10.1021/acs.analchem.3c00440