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Enhancing Top-Down Proteomics of Brain Tissue with FAIMS

Enhancing Top-Down Proteomics of Brain Tissue with FAIMS

Authors :
D. C. Bennett
Mowei Zhou
Liljiana Pasa-Tolic
A. Makaju
Vladislav A. Petyuk
James M Fulcher
Wei-Jun Qian
Ronald J. Moore
P. L. De Jager
Source :
J Proteome Res
Publication Year :
2021
Publisher :
American Chemical Society (ACS), 2021.

Abstract

Proteomic investigations of Alzheimer’s and Parkinson’s disease have provided valuable insights into neurodegenerative disorders. Thus far, these investigations have largely been restricted to bottom-up approaches, hindering the degree to which one can characterize a protein’s “intact” state. Top-down proteomics (TDP) overcomes this limitation; however, it is typically limited to observing only the most abundant proteoforms and of a relatively small size. Therefore, fractionation techniques are commonly used to reduce sample complexity. Here, we investigate gas-phase fractionation through high-field asymmetric waveform ion mobility spectrometry (FAIMS) within TDP. Utilizing a high complexity sample derived from Alzheimer’s disease (AD) brain tissue, we describe how the addition of FAIMS to TDP can robustly improve the depth of proteome coverage. For example, implementation of FAIMS with external compensation voltage (CV) stepping at −50, −40, and −30 CV could more than double the mean number of non-redundant proteoforms, genes, and proteome sequence coverage compared to without FAIMS. We also found that FAIMS can influence the transmission of proteoforms and their charge envelopes based on their size. Importantly, FAIMS enabled the identification of intact amyloid beta (Aβ) proteoforms, including the aggregation-prone Aβ(1–42) variant which is strongly linked to AD. Raw data and associated files have been deposited to the ProteomeXchange Consortium via the MassIVE data repository with data set identifier PXD023607.

Details

ISSN :
15353907 and 15353893
Volume :
20
Database :
OpenAIRE
Journal :
Journal of Proteome Research
Accession number :
edsair.doi.dedup.....f8c4bbadfb090cd5eca76d44e3c96d14
Full Text :
https://doi.org/10.1021/acs.jproteome.1c00049