%0 Journal Article %T ProteoCombiner: integrating bottom-up with top-down proteomics data for improved proteoform assessment %+ Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio) %+ Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB %A Lima, Diogo %A Dupré, Mathieu %A Duchateau, Magalie %A Gianetto, Quentin Giai %A Rey, Martial, Jean-Pierre %A Matondo, Mariette, I %A Chamot-Rooke, Julia %Z This work has been supported by the ANR [project ANR-15-CE18-0021]. It is also part of the European Joint Programme One Health EJP from the European Union’s Horizon 2020 Research and Innovation Programme [grant agreement 773830]. %< avec comité de lecture %@ 1367-4803 %J Bioinformatics %I Oxford University Press (OUP) %P btaa958 %8 2020-11-09 %D 2020 %R 10.1093/bioinformatics/btaa958 %M 33165572 %Z Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] %Z Chemical Sciences/Analytical chemistryJournal articles %X MotivationWe 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.ResultsWe 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 implementationProteoCombiner, 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). %G English %2 https://pasteur.hal.science/pasteur-03014113/document %2 https://pasteur.hal.science/pasteur-03014113/file/btaa958.pdf %L pasteur-03014113 %U https://pasteur.hal.science/pasteur-03014113 %~ PASTEUR %~ CNRS %~ OPENAIRE %~ INC-CNRS %~ TEST-HALCNRS %~ ANR %~ TEST2-HALCNRS %~ FRANCE-GENOMIQUE %~ BIOINFO_BIOSTAT_HUB