There are a number of computational tools for assigning identifications to peptide tandem mass spectra, but only a few tools, most notably ProteinProphet, for the crucial next step of integrating peptide identifications into higher-level identifications, such as proteins or modification sites. Here we describe a new program called ComByne for scoring and ranking higher-level identifications. Unlike other identification integration tools, ComByne corrects for protein lengths; it also makes use of more information, such as retention times and spectrum-to-spectrum corroborations. We compare ComByne to existing algorithms on several complex biological samples, including a sample of mouse blood plasma spiked with known concentrations of human proteins. On our samples, the combination of ComByne with our database search tool ByOnic is more sensitive than the combinations of Mascot with ProteinProphet and SEQUEST with DTASelect, with over 40% more proteins identified at 1% false discovery rate. A Web interface to our software is at http://bio.parc.xerox.com.