ProteoCombiner: integrating bottom-up with top-down proteomics data for improved proteoform assessment.

MOTIVATION: We present a high-performance software integrating shotgun with top-down proteomic data. The tool can deal with multiple experiments and search engines. Enable rapid and easy visualization, manual validation and comparison of the identified proteoform sequences including the post-translational modification characterization. RESULTS: We demonstrate the effectiveness of our approach on a large-scale Escherichia coli dataset; ProteoCombiner unambiguously shortlisted proteoforms among those identified by the multiple search engines. AVAILABILITY AND IMPLEMENTATION: ProteoCombiner, a demonstration video and user tutorial are freely available at https://proteocombiner.pasteur.fr, for academic use; all data are thus available from the ProteomeXchange consortium (identifier PXD017618). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.