Librarian: an open-access web application for high-resolution mass spectral library assembly

Confident chemical annotation in nontarget small-molecule mass spectrometry critically depends on the availability of high-quality tandem mass spectral (MS²) reference libraries. While community efforts have driven the expansion of open-access repositories, the technical burden of assembling standardized, metadata-rich records continues to limit broader participation, underscoring the need for improved computational tools to assist contributors. Here, we present Librarian , a web-based, open-access application that supports end-to-end workflows for the acquisition, assembly, and deposition of standardized MS² reference records. Through a streamlined in-browser interface and modular framework, Librarian automates batch retrieval and harmonization of chemical identifiers and metadata (via PubChem), supports design of compound mixtures for high-resolution mass spectrometry (HRMS) acquisition, and enables the assembly of MS² spectra and associated metadata into customizable records ready for deposition in public repositories (e.g. MassBank). As a demonstration, Librarian was used to generate and publicly deposit a spectral library comprising over 1,500 new MS² records, which were applied for retrospective annotation of environmental datasets. The Librarian web application is publicly accessible via the SciLifeLab Serve platform (https://librarian.serve.scilifelab.se/). Scientific contribution Librarian is an open-source application built for rapid, scalable, and automated assembly of high-resolution MS ² libraries, designed to promote the creation and open-access sharing of reference mass spectra for metabolomics, exposomics, and environmental research. Informed by open-science principles, Librarian offers a flexible end-to-end workflow compatible with multiple HRMS pre-processing tools and a streamlined interface that lowers technical barriers and facilitates broader community-driven participation in library development.