The Mass Spectrometry Development Kit (MSDK) is a Java library of algorithms for processing mass spectrometry data in metabolomics. It provides a flexible data model with Java interfaces for mass-spectrometry-related objects, and offers support for reading and writing many commonly used file formats. MSDK currently integrates a variety of algorithms for raw mass spectra filtering, feature detection, compound identification, or database search, into a single, easy-to-deploy package. The source codes of MSDK are available on GitHub under a dual GNU Lesser General Public License/Eclipse Public License, and binary artifacts of MSDK modules are deployed into the Maven Central repository.