MALDIThes

MALDIThes is a computational platform developed to streamline the analysis of data generated by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. The software combines raw spectral output with a curated thesaurus of biological and analytical terms, enabling users to annotate peaks with standardized identifiers such as protein families, metabolite classes, or post‑translational modifications. By linking peaks to the thesaurus, MALDIThes facilitates interoperability between laboratories and supports large‑scale proteomic and metabolomic projects.

The system was first released in 2018 by a consortium of academic institutions and software engineers. Early adopters in clinical microbiology and forensic science used MALDIThes to improve the speed and accuracy of bacterial strain identification. Subsequent updates incorporated machine‑learning models that predict putative compound identities from spectral patterns, increasing the proportion of confidently assigned peaks. The platform also offers batch processing, integration with laboratory information management systems, and a web‑based dashboard for real‑time result sharing.

In addition to its analytical features, MALDIThes includes a community‑curated repository of terms that follows the standards of the Unified Medical Language System (UMLS). This design allows researchers to map their findings to external ontologies, thereby enhancing data discoverability in public databases. Several studies have cited MALDIThes as a contributor to reproducibility in mass spectrometry workflows, particularly in multi‑center clinical trials where variation in peak annotation can cause significant discrepancies.

MALDIThes is distributed under an open‑source license, and its source code is available on a public repository. The project maintains an active issue tracker and a documentation portal, and it periodically releases beta versions that incorporate user feedback from the global MALDI community.