对基于质谱的多omics数据集的规范化策略的评估
Chi Yen Tseng1, Jessica A Salguero2, Joshua D Breidenbach2
1Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 84545, USA. chiyen_tseng@lanl.gov.
概括
概率系数规范化 (PQN) 和局部估计散射图平滑 (LOESS) 是多omics数据集成的顶级规范化方法. 这些方法有效地减少了错误,并保持了时间研究中的生物变异.
科学领域:
- 多omics数据集成多omics数据集成
- 生物信息学是一种生物信息学.
- 系统生物学 系统生物学
背景情况:
- 数据规范化对于准确的多omics集成至关重要,减少系统错误和增强生物信号检测.
- 现有的研究往往忽略了时间过程数据,正常化可能会对时间趋势分析产生偏见.
- 这项研究解决了在使用综合实验设计的时间多学科研究中需要强大的规范化策略的需求.
研究的目的:
- 建立一个清晰的方法来评估对多omics数据集的规范化影响.
- 为了确定最可靠的标准化技术时间课程多omics数据.
- 将传统的规范化方法与机器学习方法 (SERRF) 相比较.
主要方法:
- 对人类心肌细胞和运动神经元的代谢学,脂质学和蛋白质学数据的分析.
- 细胞在一段时间内暴露于乙胆活性化合物.
- 基于质量控制 (QC) 的标准化方法的评估包括特征一致性和差异分析 (治疗和时间效应).
主要成果:
- 概率系数规范化 (PQN) 和LOESS QC证明了代谢学和脂质学的最佳性能.
- 对于蛋白质组学来说,PQN,中位数和LOESS正常化被证明是有效的.
- 这些选择的方法始终改善了质量控制指标,并保持了关键的生物差异 (时间或治疗相关).
结论:
- 推PQN和LoessQC用于在时间多态组合中进行代谢和脂质组合的正常化.
- PQN,中位数和Loess规范化适用于类似环境中的蛋白质组学.
- 这项研究为选择可靠的规范化方法提供了一个框架,用于时间课程多学科研究.
更多相关视频
08:27Large-Scale Multi-Omics Genome-Wide Association Studies Mo-GWAS: Guidelines for Sample Preparation and Normalization
Published on: July 27, 2021
3.8K
07:34Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry UPLC-MS
Published on: March 14, 2013
12.9K
相关概念视频
01:21Mass Spectrometry: Complex Analysis
903
Mass spectrometry is an important technique for the identification of pure compounds. However, it has some limitations for the analysis of complex mixtures, often due to excessive fragmentation making the spectrum too complicated to decipher. Mass spectrometry can be combined with suitable separation methods in sequence, forming hyphenated methods, which are useful in the analysis of complex mixtures.
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...
903
01:19Mass Spectrometry: Overview
6.0K
Mass spectrometry is an analytical technique used to determine the molecular mass and molecular formula of a compound. The basic principle of mass spectrometry is to generate ions from the analyte molecule and measure these ion abundances against their molecular mass. One common type of ionization, known as electrospray ionization or EI, bombards the analyte molecules in the gas phase with high-energy electron beams. The electron beams displace an electron from the molecule and leave...
6.0K
01:13Mass Analyzers: Overview
821
The mass analyzer is a crucial component of the mass spectrometer. In the ionization chamber, the vaporized sample is bombarded with a high-energy electron beam to generate a radical cation and further fragment into neutral molecules, radicals, and cations. A series of negatively charged accelerator plates accelerate the cations into the mass analyzer. The mass analyzer separates ions according to their mass-to-charge (m/z) ratios and then directs them to the detector. The common types of mass...
821