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

We present a high-performance software integrating shotgun with top-down proteomic data. The tool can deal with multiple experiments and search engines. MOTIVATION Enable rapid and easy visualization, manual validation, and comparison of the identified proteoform sequences including the PTM characterization. RESULTS We demonstrate the effectiveness of our approach on a large-scale E. coli dataset; ProteoCombiner unambiguously shortlisted proteoforms among those identified by the multiple search engines. AVAILABILITY 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 material is available at Bioinformatics online.