方法对比

	时间序列蛋白质组学分析	时间序列 RNA-seq 差异表达
领域	生物信息学	生物信息学
方法族	Process / pipeline	Process / pipeline
起源年份	2000s (quantitative framework: Gygi et al. 1999; time-series designs: 2004–2010)	2006–2018 (principal methods established)
提出者	Multiple groups; Gygi et al. (1999) established quantitative proteomics; time-series designs emerged in the 2000s with LC-MS/MS workflows	Conesa et al. (maSigPro, 2006); extended by Fischer et al. (ImpulseDE2, 2018) and others
类型	Quantitative longitudinal omics pipeline	Computational genomics pipeline
开创性文献	Lemeer, S., & Heck, A. J. R. (2012). The phosphoproteomics data explosion. Current Opinion in Chemical Biology, 16(1–2), 1–8.	Conesa, A., Nueda, M. J., Ferrer, A., & Talon, M. (2006). maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments. Bioinformatics, 22(9), 1096–1102.
别名	longitudinal proteomics, temporal proteomics, dynamic proteomics, time-course proteomics	longitudinal RNA-seq DE analysis, temporal transcriptomics, time-course RNA-seq, dynamic DE analysis
相关	6	6
摘要	Time-series proteomics analysis quantifies protein abundance across two or more ordered time points to reveal how the proteome changes dynamically in response to stimuli, developmental stages, or disease progression. By combining mass spectrometry-based protein quantification with statistical models designed for temporal data, the method identifies proteins with significant expression trends, oscillatory patterns, or delayed responses that cannot be detected in single time-point studies.	Time-series RNA-seq differential expression analysis identifies genes whose expression levels change systematically across ordered time points — such as during development, disease progression, or response to a treatment. Unlike two-condition DE analysis, it explicitly models the temporal structure of the data, capturing dynamic gene expression trajectories rather than a single snapshot contrast. Tools such as maSigPro, ImpulseDE2, and splineTimeR have been developed specifically for this design.