Analysis of plant metabolomics data using identification-free approaches

Plant metabolomes are structurally diverse. One of the most popular techniques for sampling this diversity is liquid chromatography-mass spectrometry (LC-MS), which typically detects thousands of peaks from single organ extracts, many representing true metabolites. These peaks are usually annotated using in-house retention time or spectral libraries, in silico fragmentation libraries, and increasingly through computational techniques such as machine learning. Despite these advances, over 85% of LC-MS peaks remain unidentified, posing a major challenge for data analysis and biological interpretation. This bottleneck limits our ability to fully understand the diversity, functions, and evolution of plant metabolites. In this review, we first summarize current approaches for metabolite identification, highlighting their challenges and limitations. We further focus on alternative strategies that bypass the need for metabolite identification, allowing researchers to interpret global metabolic patterns and pinpoint key metabolite signals. These methods include molecular networking, distance-based approaches, information theory-based metrics, and discriminant analysis. Additionally, we explore their practical applications in plant science and highlight a set of useful tools to support researchers in analyzing complex plant metabolomics data. By adopting these approaches, researchers can enhance their ability to uncover new insights into plant metabolism.