Improved ranking functions for protein and modification-site identifications
There are a number of computational tools for assigning identifications to peptide tandem mass spectra, but many fewer tools for the crucial next step of integrating spectral identifications into higher level identifications, such as proteins or modification sites. In fact, many proteomics laboratories rely on expert human evaluation for the integration step. Here we describe a new program called ComByne for scoring and ranking higher level identifications. 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.
Bern, M. W. ; Goldberg, D. Improved ranking functions for protein and modification-site identifications. International Conference on Research in Computational Molecular Biology (RECOMB 2007); 2007 April 21-25; Oakland, CA. Heidelberg: Springer; 2007; LNCS 4453: 444-458.