Biomedical applications of ion mobility-enhanced data-independent acquisition-based label-free quantitative proteomics

Abstract

Mass spectrometry-based proteomics greatly benefited from recent improvements in instrument performance and the development of bioinformatics solutions facilitating the high-throughput quantification of proteins in complex biological samples. In addition to quantification approaches using stable isotope labeling, label-free quantification has emerged as the method of choice for many laboratories. Over the last years, data-independent acquisition approaches have gained increasing popularity. The integration of ion mobility separation into commercial instruments enabled researchers to achieve deep proteome coverage from limiting sample amounts. Additionally, ion mobility provides a new dimension of separation for the quantitative assessment of complex proteomes, facilitating precise label-free quantification even of highly complex samples. The present work provides a thorough overview of the combination of ion mobility and data-independent acquisition-based label-free quantification LC-MS and its applications in biomedical research.

Keywords::

• biomedical research
• data-independent acquisition
• HDMS^E
• high definition mass spectrometry
• ion mobility separation
• label-free quantification
• MS^E
• proteomics

Acknowledgements

This work was supported by grants from the Deutsche Forschungsgemeinschaft (INST 371/23–1 FUGG) and the BMBF (e:Bio Express2Present, 0316179C), as well as the Forschungszentrum Immunologie (FZI) and the Forschungszentrum Translationale Neurowissenschaften (FTN) of the Johannes Gutenberg University Mainz.

Financial & competing interests disclosure

This work was funded by Deutsche Forschungsgemeinschaft (INST 371/23–1 FUGG), BMBF (e:Bio Express2Present, 0316179C), Forschungszentrum Immunologie (FZI) and the Forschungszentrum Translationale Neurowissenschaften (FTN) of the Johannes Gutenberg University Mainz. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Key issues

• Label-free quantification is a key technology in biomedical research, which can be applied to the relative quantification of many samples in parallel, including ex vivo and patient samples. Performance is theoretically limited only by instrument time and platform stability.

• Providing a high duty cycle, data-independent acquisition (DIA) schemes, such as MS^E, are perfectly suited for feature-based label-free quantification.

• Ion mobility separation (IMS) has been recently integrated into MS^E-based workflows and has been successfully applied to a number of quantitative proteomics studies.

• Separating gas-phase ions based on their size and shape, IMS is an analytical technique that is complementary to MS.

• IMS increases overall system peak capacity while concomitantly reducing chimeric and composite interferences.

• Label-free quantification approaches can greatly benefit from the integration of IMS, which offers novel possibilities in both qualitative and quantitative assessment of proteomics data.

• The integration of IMS substantially increases proteome coverage. Future improvements in system peak capacity will lead to a concomitant increase in the number of identifiable and quantifiable proteins and peptides in DIA-based proteomics.

Notes