Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, New York.
Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, New York, New York.
Mass Spectrom Rev. 2019 Nov;38(6):461-482. doi: 10.1002/mas.21595. Epub 2019 Mar 28.
The rapidly-advancing field of pharmaceutical and clinical research calls for systematic, molecular-level characterization of complex biological systems. To this end, quantitative proteomics represents a powerful tool but an optimal solution for reliable large-cohort proteomics analysis, as frequently involved in pharmaceutical/clinical investigations, is urgently needed. Large-cohort analysis remains challenging owing to the deteriorating quantitative quality and snowballing missing data and false-positive discovery of altered proteins when sample size increases. MS1 ion current-based methods, which have become an important class of label-free quantification techniques during the past decade, show considerable potential to achieve reproducible protein measurements in large cohorts with high quantitative accuracy/precision. Nonetheless, in order to fully unleash this potential, several critical prerequisites should be met. Here we provide an overview of the rationale of MS1-based strategies and then important considerations for experimental and data processing techniques, with the emphasis on (i) efficient and reproducible sample preparation and LC separation; (ii) sensitive, selective and high-resolution MS detection; iii)accurate chromatographic alignment; (iv) sensitive and selective generation of quantitative features; and (v) optimal post-feature-generation data quality control. Prominent technical developments in these aspects are discussed. Finally, we reviewed applications of MS1-based strategy in disease mechanism studies, biomarker discovery, and pharmaceutical investigations.
药物和临床研究领域的快速发展需要对复杂的生物系统进行系统的、分子水平的描述。为此，定量蛋白质组学是一种强大的工具，但对于可靠的大样本蛋白质组学分析（如在药物/临床研究中经常涉及的），仍迫切需要一个最佳的解决方案。由于随着样本量的增加，定量质量恶化、丢失数据呈雪球式增加以及改变蛋白的假阳性发现等问题，大样本分析仍然具有挑战性。在过去十年中，基于 MS1 离子电流的方法已成为一种重要的无标记定量技术，它们在大样本中具有实现可重复的蛋白质测量的巨大潜力，并且具有较高的定量准确性和精密度。尽管如此，为了充分发挥这种潜力，仍需要满足一些关键的前提条件。本文概述了基于 MS1 的策略的基本原理，然后重点讨论了实验和数据处理技术的重要考虑因素，包括：（i）高效且可重复的样品制备和 LC 分离；（ii）灵敏、选择性和高分辨率的 MS 检测；（iii）准确的色谱对准；（iv）灵敏和选择性的定量特征生成；以及（v）最佳的特征生成后数据质量控制。讨论了这些方面的突出技术进展。最后，我们回顾了基于 MS1 的策略在疾病机制研究、生物标志物发现和药物研究中的应用。
