Tian Huohuan, Tao Ze, Zhang Wanli, Chen Yuzhe, Su Tao, Wang Xinyuan, Yang Hao, Cai Hao, Liu Shuyun, Zhang Yi, Zhang Yong
Department of Respiratory & Critical Care Medicine, Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu 610041, China.
Transplant Center and NHC Key Lab of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu 610041, China.
J Proteome Res. 2025 Jan 3;24(1):134-143. doi: 10.1021/acs.jproteome.4c00545. Epub 2024 Dec 13.
Human plasma proteomic and glycoproteomic analyses have emerged as an alternate avenue to identify disease biomarkers and therapeutic approaches. However, the vast number of high-abundance proteins in plasma can cause mass spectrometry (MS) suppression, which makes it challenging to detect low-abundance proteins (LAP). Currently, immunoaffinity-based depletion methods and strategies involving nanomaterial protein coronas have been developed to remove high-abundance proteins (HAP) and enhance the depth of plasma protein identification. Despite these advancements, there is a lack of systematic comparison and evaluation of the qualitative and quantitative effects of different strategies on the human plasma proteome and glycoproteome. In this study, we evaluated the performance of four depletion methods including combinatorial peptide ligand libraries (CPLL), Top 2, Top 14, and the nanomaterial protein corona formed by magnetic nanoparticles (MN) in both plasma proteomics and -glycoproteomics. Compared to the CPLL, Top 2, and Top 14 strategies, the MN approach significantly increased the number of identified peptides and proteins. However, it demonstrated a relatively lower efficacy in identifying intact -glycopeptides and -glycoproteins. In contrast, the immunoaffinity-based depletion methods are better suited to glycoproteomics due to higher identification numbers. We believe that this work provides valuable insights and options for various research objectives, as well as clinical applications.
人类血浆蛋白质组学和糖蛋白质组学分析已成为识别疾病生物标志物和治疗方法的另一条途径。然而，血浆中大量的高丰度蛋白质会导致质谱（MS）抑制，这使得检测低丰度蛋白质（LAP）具有挑战性。目前，已开发出基于免疫亲和的去除方法以及涉及纳米材料蛋白质冠的策略，以去除高丰度蛋白质（HAP）并提高血浆蛋白质鉴定的深度。尽管有这些进展，但缺乏对不同策略对人类血浆蛋白质组和糖蛋白质组的定性和定量影响的系统比较和评估。在本研究中，我们评估了四种去除方法的性能，包括组合肽配体库（CPLL）、Top 2、Top 14以及由磁性纳米颗粒（MN）形成的纳米材料蛋白质冠在血浆蛋白质组学和糖蛋白质组学中的性能。与CPLL、Top 2和Top 14策略相比，MN方法显著增加了鉴定出的肽和蛋白质的数量。然而，它在鉴定完整糖肽和糖蛋白方面表现出相对较低的功效。相比之下，基于免疫亲和的去除方法由于鉴定数量较多，更适合糖蛋白质组学。我们相信这项工作为各种研究目标以及临床应用提供了有价值的见解和选择。
