DiLeu Isobaric Labeling Coupled with Limited Proteolysis Mass Spectrometry for High-Throughput Profiling of Protein Structural Changes in Alzheimer’s Disease

Abstract

High-throughput quantitative analysis of protein conformational changes has a profound impact on our understanding of the pathological mechanisms of Alzheimer’s disease (AD). To establish an effective workflow enabling quantitative analysis of changes in protein conformation within multiple samples simultaneously, here we report the combination of N,N-dimethyl leucine (DiLeu) isobaric tag labeling with limited proteolysis mass spectrometry (DiLeu-LiP-MS) for high-throughput structural protein quantitation in serum samples collected from AD patients and control donors. Twenty-three proteins were discovered to undergo structural changes, mapping to 35 unique conformotypic peptides with significant changes between the AD group and the control group. Seven out of 23 proteins, including CO3, CO9, C4BPA, APOA1, APOA4, C1R, and APOA, exhibited a potential correlation with AD. Moreover, we found that complement proteins (e.g., CO3, CO9, and C4BPA) related to AD exhibited elevated levels in the AD group compared to those in the control group. These results provide evidence that the established DiLeu-LiP-MS method can be used for high-throughput structural protein quantitation, which also showed great potential in achieving large-scale and in-depth quantitative analysis of protein conformational changes in other biological systems.

A Tutorial Review of Labeling Methods in Mass Spectrometry-Based Quantitative Proteomics

“…Mass spectrometry (MS) has been a cornerstone in the field of proteomics, offering unparalleled insights into complex protein information within biological systems. Over the past decades, MS-based proteomics has facilitated accurate genome-wide quantification of protein changes across multiple biological states in a single experiment. , This evolution is largely attributed to the advancements in labeling techniques, which have markedly enhanced the precision, accuracy, and throughput of quantitative proteomic studies. , Consequently, these labeling techniques have broadened the scope and capabilities of proteomic research, catalyzing significant progress in key applications such as protein structural elucidation, − biomarker discovery, − and drug development. − …”