MetaXtract: Extracting Metadata from Raw Files for FAIR Data Practices and Workflow Optimisation

Mass spectrometry (MS) experiments generate rich acquisition metadata that are essential for reproducibility, data sharing, and quality control (QC). Because these metadata are typically stored only in vendor-specific formats, they often remain difficult to access. MetaXtract is a lightweight tool that extracts detailed parameters directly from Thermo Fisher raw files and exposes them in structured, tabular formats. By capturing sample information, LC-MS method settings, and scan-level metrics such as retention time, total ion current, and ion injection time, MetaXtract increases transparency and ensures that essential acquisition details accompany published data and results in easy readable form. This supports FAIR data practices by improving the findability, accessibility, interoperability, and reusability of MS datasets, thereby increasing the value of deposition in public repositories. The importance of such metadata accessibility was recently highlighted by the crosslinking mass spectrometry community in efforts to advance FAIR data principles, and it extends to MS-based omics approaches more broadly. Beyond data sharing, the tool streamlines QC and troubleshooting through simple visualisations of MS1/MS2 scans and enables integration into automated pipelines. By embedding acquisition parameters into routine data handling, MetaXtract strengthens reproducibility, optimises method development, and supports large-scale applications, including machine learning and secondary data analysis.