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

Abstract : 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).
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https://hal-pasteur.archives-ouvertes.fr/pasteur-03014113
Contributor : Martial Rey <>
Submitted on : Thursday, November 19, 2020 - 11:58:39 AM
Last modification on : Wednesday, June 9, 2021 - 8:10:01 AM
Long-term archiving on: : Saturday, February 20, 2021 - 7:04:42 PM

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Diogo Lima, Mathieu Dupré, Magalie Duchateau, Quentin Giai Gianetto, Martial Rey, et al.. ProteoCombiner: integrating bottom-up with top-down proteomics data for improved proteoform assessment. Bioinformatics, Oxford University Press (OUP), 2020, pp.btaa958. ⟨10.1093/bioinformatics/btaa958⟩. ⟨pasteur-03014113⟩

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