Methoden vergleichen

	Zeitreihen-Proteomik-Analyse	RNA-seq Differential Expression
Fachgebiet	Bioinformatik	Bioinformatik
Familie	Process / pipeline	Process / pipeline
Entstehungsjahr	2000s (quantitative framework: Gygi et al. 1999; time-series designs: 2004–2010)	2008–2010 (RNA-seq DE methodology established)
Urheber	Multiple groups; Gygi et al. (1999) established quantitative proteomics; time-series designs emerged in the 2000s with LC-MS/MS workflows	Multiple groups; foundational methods from Anders & Huber (DESeq, 2010), Robinson, McCarthy & Smyth (edgeR, 2010)
Typ	Quantitative longitudinal omics pipeline	Quantitative genomics pipeline
Wegweisende Quelle	Lemeer, S., & Heck, A. J. R. (2012). The phosphoproteomics data explosion. Current Opinion in Chemical Biology, 16(1–2), 1–8.	Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12), 550.
Aliasnamen	longitudinal proteomics, temporal proteomics, dynamic proteomics, time-course proteomics	RNA-seq DE analysis, transcriptomic differential expression, bulk RNA-seq DE, DEA
Verwandt	6	6
Zusammenfassung	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.	RNA-seq differential expression (DE) analysis identifies genes whose transcript abundance differs significantly between two or more biological conditions — for example, treated versus control, or diseased versus healthy tissue. Starting from raw sequencing reads, the pipeline moves through alignment, count-based normalization, statistical modeling of count dispersion, hypothesis testing, and multiple-testing correction to produce a ranked list of differentially expressed genes accompanied by fold-change estimates and adjusted p-values.