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

ABSTRACT: 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. 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. 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). Supplementary data are available at Bioinformatics online.

SUBMITTER: Dhenin J

PROVIDER: S-EPMC8796372 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature

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

Dhenin Jonathan J Borges Lima Diogo D Dupré Mathieu M Chamot-Rooke Julia J

Bioinformatics (Oxford, England) 20220101 4

<h4>Motivation</h4>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 (tandem mass spectrometry) analysis of intact proteins. Our tool can process data obtained from various deconvolution and fragment assignment software.<h4>Results</h4>We demonstrate that TDFragMapper can rapidly highlight the experimental fragmentation parameters that are critical to the charac ...[more]

PMID: 34792554

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