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- Title
ProteoCombiner: integrating bottom-up with top-down proteomics data for improved proteoform assessment.
- Authors
Lima, Diogo B; Dupré, Mathieu; Duchateau, Magalie; Gianetto, Quentin Giai; Rey, Martial; Matondo, Mariette; Chamot-Rooke, Julia
- 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). Supplementary information Supplementary data are available at Bioinformatics online.
- Subjects
PROTEOMICS; POST-translational modification; INTEGRATED software; ESCHERICHIA coli; SEARCH engines
- Publication
Bioinformatics, 2021, Vol 37, Issue 15, p2206
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btaa958