"Applications of the MSFragger algorithm in mass spectrometry-based proteomics"
Abstract
MSFragger enables fast and comprehensive database searching by performing mass-tolerant searches 150X faster than conventional tools. These mass-tolerant searches enable the simultaneous identification of both unmodified and modified peptides in mass-spectrometry experiments. By comparing narrow-window and mass-tolerant search results, we demonstrate that false discovery rates are severely underestimated by the popular target-decoy strategy due to unaccounted-for modified peptides. We profiled large scale proteomics studies to reveal dramatic differences in modification rates and numerous unknown chemical modifications. Using an adaption of the fragment index algorithm in MSFragger, we are developing strategies for querying large repositories of proteomics data in real time.
