LC-MS Data Processing Using OpenMS

Liquid chromatography-mass spectrometry (LC-MS) is a cornerstone of metabolomics, enabling detailed analysis of complex biological samples. Untargeted approaches, however, face challenges in handling complex data and ensuring scalability. UmetaFlow, built on the OpenMS platform, addresses these challenges through a unique re-quantification step for low-abundance metabolites and a suite of complementary annotation tools. Available in four formats, from command-line tools to an interactive WebApp, UmetaFlow supports both high-throughput automation and manual data exploration. This chapter provides a step-by-step guide to UmetaFlow and its applications.