There isn’t a single “recommended” commercial software for database searching in a GMP environment, as compliance is not determined by the specific tool itself, but by how it is implemented, validated, and controlled.
Several well‑known proteomics database search engines are commonly used in LC‑MS workflows (e.g. vendor‑provided software or third‑party platforms), but for GMP use, the key requirement is that the selected software is validated for its intended use, with appropriate controls for data integrity, audit trails, version management, and traceability.

In practice, this means that database search is performed within a validated data processing workflow, where parameters are predefined, results are reviewable, and all steps are documented and reproducible. The focus is therefore on ensuring the entire data analysis pipeline meets regulatory expectations, rather than relying on a specific software label.

Thomas Kofoed, PhD, CEO of Alphalyse in Denmark, discussed key factors in implementing GMP-compatible LC-MS methods for release assays and highlighted successful cases where this approach has replaced traditional ELISA methods. Don’t miss his presentation and expert insights at the panel discussion.