TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization

Abstract

Summary: Top-down mass spectrometry enables the observation of whole complex proteoforms in biological samples and provides crucial information complementary to bottom-up mass spectrometry. Because of the complexity of top-down mass spectra and proteoforms, it is a challenging problem to efficiently interpret top-down tandem mass spectra in high-throughput proteome-level proteomics studies. We present TopPIC, a tool that efficiently identifies and characterizes complex proteoforms with unknown primary structure alterations, such as amino acid mutations and post-translational modifications, by searching top-down tandem mass spectra against a protein database., Availability and Implementation: http://proteomics.informatics.iupui.edu/software/toppic/, Contact: xwliu@iupui.edu, Supplementary information: Supplementary data are available at Bioinformatics online.