Abdi, H.; Ambaw, Y.; Chitraju, C.; Singh, S.; Zon, W. L.; Farese, R.; Walther, T. C.

Advances in mass spectrometry (MS)-based lipidomics have led to a surge in data volume, underscoring a need for robust tools to evaluate and visualize these data comprehensively. Current workflows are often hampered by manual spreadsheet handling and insufficient assessment of data quality prior to analysis. Here, we introduce LipidCruncher, an open-source, web-based platform designed to process, visualize, and analyze lipidomic data with high efficiency and rigor. LipidCruncher consolidates key steps of the workflow, including data standardization, normalization, and stringent quality control to identify anomalies. The platform also provides advanced visualization and analysis tools, such as volcano plots, lipid saturation profiles, pathway mapping, and lipid heatmaps, that enable detailed and holistic data exploration. To demonstrate LipidCruncher utility, we analyzed lipidomic data from adipose tissue of mice lacking the triacylglycerol synthesis enzymes DGAT1 and DGAT2. We anticipate that LipidCruncher will be a valuable and user-friendly tool for standardizing and analyzing lipidomics data.