Updated project metadata. We developed a method that allows measuring the stable carbon isotope composition of individual species in microbial communities using metaproteomics. We call this methods “Direct Protein-SIF”. We validated and tested the method extensively using pure cultures (PXD006762) and mock communities (PXD006118, https://www.ebi.ac.uk/pride/archive/projects/PXD006118). As a case study we applied Direct Protein-SIF to the Olavius algarvensis symbiosis. Olavius algarvensis is a marine worm that lives in shallow-water sediments off the coast of Elba, Italy. The worm has no digestive and excretory system, instead it harbors five bacterial symbionts that fulfill its nutritional and waste recycling needs (http://www.pnas.org/content/109/19/E1173.short). For this project we generated metaproteomes of 14 O. algarvensis individuals. A total of 18 LC-MS/MS runs were generated. For Direct Protein-SIF the data from all runs was combined. In this submission we are including the Direct Protein-SIF specific isotope pattern file as well as the .mzML files and PSM file required as input for the Direct Protein-SIF software (Calis-p). In addition to the Olavius algarvensis samples a protein reference material (MKH files) was measured. The respective .raw files and isotopic pattern files are available through project PXD006762 (see publication for details on how the reference material is used to calibrate the method).