University of Dundee NPAW 2025

Metadata is essential for linking experimental workflows and biological traits with numerical data, particularly as researchers analyze large datasets. Historically, the proteomics community has faced challenges with dataset integration due to poor metadata management. In 2021, the SDRF-proteomics format was introduced to improve this, but adoption has been limited due to lacking tools that can utilize and compose the file format. To address these issues, I developed Cupcake, an open-source Laboratory Information Management System specifically designed for Mass Spectrometry Core Facilities. Cupcake streamlines job submissions with an extended SDRF schema, pre-annotating MS instruments and enhancing metadata integration. It also manages instrument maintenance and alerts for upkeep. Additionally, Cupcake’s lab notebook allows compilation of metadata throughout experiments and allows for easy export for stock management. Our aim is that, regardless of intention for publication, every dataset generated through the MS Facility will include comprehensive metadata, ensuring their usefulness for future machine learning-based large-scale analysis.