MixDB

Summary

In high-throughput proteomics, the development of computational methods and novel experimental strategies and their application often rely on each other. However, most computational approaches still make the assumption that each MS/MS spectrum comes from one peptide while there are numeroussituations where one MS/MS spectrum can contain fragment ions corresponding to two or more peptides. Examples include mixture spectra from co-eluting peptides in complex samples, spectra generated from data-independent acquisition methods and spectra from peptides with complex PTMs. We propose a new database search tool (MixDB) that is able to identify mixture MS/MS spectra from more than one peptide. We show that peptides can be reliably identified with up to 95% accuracy from mixture spectra while considering only a small fraction of all possible peptide pairs (speedup of four orders of magnitude). Comparison with current database search methods indicates that our approach has better or comparable sensitivity and precision at identifying single-peptide spectra while being able to identify 20% more mixture spectra at significantly higher precision.