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, offline fractionation techniques are commonly used to reduce sample complexity, limiting throughput. A higher throughput alternative is online fractionation, such as gas phase high-field asymmetric waveform ion mobility spectrometry (FAIMS). Utilizing a high complexity sample derived from Alzheimer's disease brain tissue, we describe how the addition of FAIMS to TDP can robustly improve the depth of proteome coverage. For example, implementation of FAIMS at -50 compensation voltage (CV) more than doubled the mean number of non-redundant proteoforms observed (1,833 ± 17, n = 3), compared to without (754 ± 35 proteoforms). We also found 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 Alzheimer′s disease.

中文翻译：

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利用FAIMS增强脑组织的自上而下的蛋白质组学

蛋白质组学研究阿尔茨海默氏症和帕金森氏症，为神经退行性疾病提供了宝贵的见解。迄今为止，这些研究很大程度上仅限于自下而上的方法，从而阻碍了人们可以表征蛋白质“完整”状态的程度。自上而下的蛋白质组学（TDP）克服了此限制，但是它通常仅限于仅观察最丰富的蛋白形体，并且尺寸相对较小。因此，离线分离技术通常用于降低样品的复杂性，从而限制了通量。更高通量的替代方法是在线分馏，例如气相高场非对称波形离子迁移谱（FAIMS）。利用源自阿尔茨海默氏病脑组织的高复杂度样本，我们描述了如何将FAIMS添加到TDP可以有效地改善蛋白质组覆盖的深度。例如，在没有补偿（754±35）的情况下，在-50补偿电压（CV）下实施FAIMS可以使观察到的非冗余蛋白的平均数量（1,833±17，n = 3）增加一倍以上。我们还发现FAIMS可以根据其大小影响蛋白形式及其电荷包膜的传递。重要的是，FAIMS能够鉴定完整的淀粉样蛋白（Aβ）蛋白形式，包括易于聚集的Aβ 我们还发现FAIMS可以根据其大小影响蛋白形式及其电荷包膜的传递。重要的是，FAIMS能够鉴定完整的淀粉样蛋白（Aβ）蛋白形式，包括易于聚集的Aβ 我们还发现FAIMS可以根据其大小影响蛋白形式及其电荷包膜的传递。重要的是，FAIMS能够鉴定完整的淀粉样蛋白（Aβ）蛋白形式，包括易于聚集的Aβ与阿尔茨海默氏病密切相关的_1-42变体。