Related Experiment Video
Updated: Oct 13, 2025
Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
Published on: August 19, 2025
TDFragMapper: a visualization tool for evaluating experimental parameters in top-down proteomics
Jonathan Dhenin1,2, Diogo Borges Lima3, Mathieu Dupré1
1Mass Spectrometry for Biology Unit, Institut Pasteur, Université de Paris, CNRS USR2000, Paris, France.
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 (tandem mass spectrometry) 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 And Implementation:
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 Information:
Supplementary data are available at Bioinformatics online.
