ProteoCombiner is a high-performance software integrating shotgun with top-down proteomic data. The tool can deal with multiple experiments and search engines. It enables rapid and easy visualization, manual validation, and comparison of the identified proteoform sequences including the PTM characterization. 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. ProteoCombiner, a demonstration video and user tutorial are freely available at https://proteocombiner.pasteur.fr, for academic use; all data are available from the ProteomeXchange consortium (identifier PXD017618).
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