TDFragMapper: a visualization tool for evaluating experimental parameters in top-down proteomics

Jonathan Dhenin (1, 2) , Diogo B Lima (3) , Mathieu Dupré (1) , Julia Chamot-Rooke (1)

1 UTechS MSBio - Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology
2 UPCité - Université Paris Cité
3 FMP - Leibniz Forschungsinstitut für Molekulare Pharmakolgie = Leibniz Institute for Molecular Pharmacology [Berlin, Allemagne]

Motivation We present a new software-tool allowing an easy visualization of fragment ions and thus a rapid evaluation of key experimental parameters on the sequence coverage obtained for the MS/MS analysis of intact proteins. Our tool can process data obtained from various deconvolution and fragment assignment software. Results We demonstrate that TDFragMapper can rapidly highlight the experimental fragmentation parameters that are critical to the characterization of intact proteins of various size using top-down proteomics. Availability TDFragMapper, a demonstration video and user tutorial are freely available for academic use at https://msbio.pasteur.fr/tdfragmapper; all data are thus available from the ProteomeXchange consortium (identifier PXD024643).

Domaines: Bio-Informatique, Biologie Systémique [q-bio.QM]

Jonathan Dhenin, Diogo B Lima, Mathieu Dupré, Julia Chamot-Rooke. TDFragMapper: a visualization tool for evaluating experimental parameters in top-down proteomics. Bioinformatics, 2021, pp.btab784. ⟨10.1093/bioinformatics/btab784⟩. ⟨pasteur-03441695⟩