Top-Down Garbage Collector: a tool for selecting high-quality top-down proteomics mass spectra.

MOTIVATION: We present the first tool for unbiased quality control of top-down proteomics datasets. Our tool can select high-quality top-down proteomics spectra, serve as a gateway for building top-down spectral libraries and, ultimately, improve identification rates. RESULTS: We demonstrate that a twofold rate increase for two E. coli top-down proteomics datasets may be achievable. AVAILABILITY AND IMPLEMENTATION: http://patternlabforproteomics.org/tdgc, freely available for academic use. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.