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Analysis of differential strategies to enhance detection of low-abundance proteins in the bovine serum proteome.
Animal Science Journal ( IF 1.7 ) Pub Date : 2020-06-23 , DOI: 10.1111/asj.13388
Kasey M Schalich 1 , Anthony W Herren 2 , Vimal Selvaraj 1
Affiliation  

Serum‐based biomarkers hold propitious applications for addressing livestock health, and management. However, discovery of protein biomarkers in complex biological fluids like serum is wholly intractable due to the large dynamic range of protein concentrations; that is, ˜10–12 high abundance proteins constitute >90% of the total protein content and effectively mask proteomic detection of low‐abundance biomarkers. Toward addressing this limitation, we test a continuous elution size‐based fractionation method, and two approaches that use affinity interaction‐based separation of proteins in preparing bovine serum, and compare liquid chromatography tandem mass spectrometry protein identification to neat serum. Our results identify the high‐abundance proteins in bovine serum, and demonstrate dynamic range compression and improved protein identification with the different enrichment methods. Although these findings indicate the highest protein number identified in bovine serum (445 proteins, all methods combined), and by any single sample processing method (312 proteins) to date, they still remain lower than levels deemed necessary for biomarker discovery. As such, this investigation revealed limitations to resolving the bovine serum proteome, and the need for species‐specific tools for immunodepleting high‐abundance proteins. In concert, this study represents a step toward advancing sample preparation methods for bovine serum biomarker identification.

中文翻译:

分析增强牛血清蛋白质组中低丰度蛋白质检测的差异策略。

基于血清的生物标志物在解决牲畜健康和管理方面具有良好的应用前景。然而,由于蛋白质浓度的动态范围很大,在血清等复杂生物流体中发现蛋白质生物标志物是完全棘手的;也就是说,约 10-12 种高丰度蛋白质占总蛋白质含量的 90% 以上,并有效地掩盖了低丰度生物标志物的蛋白质组学检测。为了解决这一局限性,我们测试了基于连续洗脱大小的分级分离方法,以及两种使用基于亲和力相互作用的蛋白质分离方法来制备牛血清,并将液相色谱串联质谱法蛋白质鉴定与纯血清进行了比较。我们的结果确定了牛血清中的高丰度蛋白质,并通过不同的富集方法展示动态范围压缩和改进的蛋白质鉴定。尽管这些发现表明迄今为止在牛血清中鉴定出的蛋白质数量最多(445 种蛋白质,所有方法相结合),并且通过任何单一样品处理方法(312 种蛋白质),它们仍然低于生物标志物发现所需的水平。因此,这项调查揭示了解决牛血清蛋白质组的局限性,以及对免疫耗竭高丰度蛋白质的物种特异性工具的需求。总之,这项研究代表了朝着推进用于牛血清生物标志物鉴定的样品制备方法迈出的一步。迄今为止,通过任何单一样本处理方法(312 种蛋白质),它们仍然低于生物标志物发现所需的水平。因此,这项调查揭示了解决牛血清蛋白质组的局限性,以及对免疫耗竭高丰度蛋白质的物种特异性工具的需求。总之,这项研究代表了朝着推进用于牛血清生物标志物鉴定的样品制备方法迈出的一步。迄今为止,通过任何单一样本处理方法(312 种蛋白质),它们仍然低于生物标志物发现所需的水平。因此,这项调查揭示了解决牛血清蛋白质组的局限性,以及对免疫耗竭高丰度蛋白质的物种特异性工具的需求。总之,这项研究代表了朝着推进用于牛血清生物标志物鉴定的样品制备方法迈出的一步。
更新日期:2020-06-24
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