TL;DR
This chapter presents a step-by-step pipeline for the statistical and computational analysis of such data, oriented and generalizable to any mass spectrometry-derived proteomic dataset, facilitating an end-to-end analysis from raw proteomic data to the biological interpretation.
The demand for user-friendly applications to support biologists in analyzing high-throughput proteomics data remains a pressing challenge. Given the complexity and the multiple intermediate steps involved, this process is time-consuming and often requires specialized computational skills. To simplify and accelerate the...
A scalable workflow for the deep proteomic analysis of low- to ultralow-input samples by systematically optimizing a widely adopted Orbitrap and UHPLC platform to maximize sensitivity, precision, and throughput is developed.
ProteoScopeR is an R package and Shiny application that connects decisions in a traceable workflow and complements downstream exploration in xOmicsShiny and describes sensitivity to analytical choices rather than identify a universally superior method.
Liquid chromatography-mass spectrometry (LC-MS) is a key technology in metabolomics, enabling high-throughput detection of small molecules across diverse biological samples. However, raw LC-MS data are complex, requiring careful preprocessing to ensure accurate and reproducible feature detection. This chapter introduce...
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