Analysis of 1508 Plasma Samples by Capillary-Flow Data-Independent Acquisition Profiles Proteomics of Weight Loss and Maintenance
Analysis of 1508 Plasma Samples by Capillary-Flow Data-Independent Acquisition Profiles Proteomics of Weight Loss and Maintenance
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DOI：
10.1074/mcp.ra118.001288
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发表时间：
2019-06-01
影响因子：
7
通讯作者：
Reiter, Lukas
中科院分区：
文献类型：
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作者：
Bruderer, Roland;Muntel, Jan;Reiter, Lukas
血浆蛋白质组的全面、高通量分析具有实现个体健康状态的整体分析的潜力。根据我们自己的经验和最近的大规模等离子体质谱（MS）为基础的蛋白质组学研究的评价，我们确定了两个突出的挑战：缓慢和微妙的纳米流液相色谱（LC）和数据依赖性采集（DDA）的识别的不可重复性。我们确定了一个最佳的解决方案，减少这些限制与强大的毛细管流数据独立采集（DIA）MS。这个平台可以测量31血浆蛋白质组每天。使用这种设置，我们获得了包括1508个样品的饮食、肥胖和饮食基因（DiOGenes）的大规模血浆研究。为了证明耐用性，在单个分析柱上实现了完整采集。总共，565个蛋白质（459个被鉴定为具有两个或更多个肽序列）以74%的数据集完整性进行了分析。平均408个蛋白质（5246个肽）被确定为每次采集（319个蛋白质在所有采集的90%）。使用定期采集的34个质控样本池评估了工作流程重现性，结果数据集完整性为92%，蛋白质测量CV为10.9%。20种载脂蛋白的谱图显示出明显的变化。体重减轻和体重维持对低度炎症以及类固醇激素和脂质代谢产生持续影响，表明有益效果。与其他大规模血浆体重减轻研究的比较证明了所鉴定的生物标志物候选物的高稳健性和质量。非酶糖化的跟踪表明，在体重维持阶段，糖化延迟轻微降低。使用稳定同位素参考，我们可以直接和绝对定量DIA中的60种蛋白质。总之，我们在此介绍了第一个大规模的血浆DIA研究和迄今为止最大的临床研究蛋白质组学研究之一。这种快速和强大的工作流程的应用具有极大的潜力，以推进血浆中生物标志物的发现。
Comprehensive, high throughput analysis of the plasma proteome has the potential to enable holistic analysis of the health state of an individual. Based on our own experience and the evaluation of recent large-scale plasma mass spectrometry (MS) based proteomic studies, we identified two outstanding challenges: slow and delicate nano-flow liquid chromatography (LC) and irreproducibility of identification of data-dependent acquisition (DDA). We determined an optimal solution reducing these limitations with robust capillary-flow data-independent acquisition (DIA) MS. This platform can measure 31 plasma proteomes per day. Using this setup, we acquired a largescale plasma study of the diet, obesity and genes dietary (DiOGenes) comprising 1508 samples. Proving the robustness, the complete acquisition was achieved on a single analytical column. Totally, 565 proteins (459 identified with two or more peptide sequences) were profiled with 74% data set completeness. On average 408 proteins (5246 peptides) were identified per acquisition (319 proteins in 90% of all acquisitions). The workflow reproducibility was assessed using 34 quality control pools acquired at regular intervals, resulting in 92% data set completeness with CVs for protein measurements of 10.9%. The profiles of 20 apolipoproteins could be profiled revealing distinct changes. The weight loss and weight maintenance resulted in sustained effects on low-grade inflammation, as well as steroid hormone and lipid metabolism, indicating beneficial effects. Comparison to other largescale plasma weight loss studies demonstrated high robustness and quality of biomarker candidates identified. Tracking of nonenzymatic glycation indicated a delayed, slight reduction of glycation in the weight maintenance phase. Using stable-isotope-references, we could directly and absolutely quantify 60 proteins in the DIA. In conclusion, we present herein the first large-scale plasma DIA study and one of the largest clinical research proteomic studies to date. Application of this fast and robust workflow has great potential to advance biomarker discovery in plasma.