Abstract Summary Unipept is an open source web application that is designed for metaproteomics analysis with a focus on interactive datavisualization. It is underpinned by a fast index built from UniProtKB and the NCBI taxonomy that enables quick retrieval of all UniProt entries in which a given tryptic peptide occurs. Unipept version 2.4 introduced web services that provide programmatic access to the metaproteomics analysis features. This enables integration of Unipept functionality in custom applications and data processing pipelines. Availability and implementation: The web services are freely available at http://api.unipept.ugent.be and are open sourced under the MIT license. Contact: Unipept@ugent.be Supplementary information: Supplementary data are available at Bioinformatics online.