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

Dhenin, Jonathan; Lima, Diogo Borges; Dupré, Mathieu; Chamot‐Rooke, Julia

doi:10.1093/bioinformatics/btab784

Cited by 4 publications

(5 citation statements)

References 7 publications

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“…Only b‐ and y‐ions were considered for CID and HCD fragmentations, while b‐, c‐, y‐ and z‐ions were searched for EThcD. TDFragMapper 35 was used for further visualization and comparison of fragmentation results. Lists of assigned fragments were exported from ProSight Lite and used with deconvolved data and the protein sequence as input for TDFragMapper.…”

Section: Methodsmentioning

confidence: 99%

A multiparameter optimization in middle‐down analysis of monoclonal antibodies by LC–MS/MS

et al. 2023

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In antibody-based drug research, a complete characterization of antibody proteoforms covering both the amino acid sequence and all posttranslational modifications remains a major concern. The usual mass spectrometry-based approach to achieve this goal is bottom-up proteomics, which relies on the digestion of antibodies but does not allow the diversity of proteoforms to be assessed. Middle-down and topdown approaches have recently emerged as attractive alternatives but are not yet mastered and thus used in routine by many analytical chemistry laboratories. The work described here aims at providing guidelines to achieve the best sequence coverage for the fragmentation of intact light and heavy chains generated from a simple reduction of intact antibodies using Orbitrap mass spectrometry. Three parameters were found crucial to this aim: the use of an electron-based activation technique, the multiplex selection of precursor ions of different charge states, and the combination of replicates.

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Section: Methodsmentioning

confidence: 99%

A multiparameter optimization in middle‐down analysis of monoclonal antibodies by LC–MS/MS

et al. 2023

Self Cite

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“…Only b- and y-ions were considered for CID and HCD fragmentations while b-, c-, y- and z-ions were searched for EThcD. TDFragMapper 35 was used for further visualization and comparison of fragmentation results. Lists of assigned fragments were exported from ProSight Lite and used with deconvoluted data and the protein sequence as input for TDFragMapper.…”

Section: Methodsmentioning

confidence: 99%

A multi-parameter optimization in middle-down analysis of monoclonal antibodies by LC-MS/MS

Dhenin

Dupré

Druart

et al. 2022

Preprint

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In antibody-based drug research, regulatory agencies request a complete characterization of antibody proteoforms covering both the amino acid sequence and all post-translational modifications. The usual mass spectrometry-based approach to achieve this goal is bottom-up proteomics, which relies on the digestion of antibodies, but does not allow the diversity of proteoforms to be assessed. Middle-down and top-down approaches have recently emerged as attractive alternatives but are not yet mastered and thus used in routine by many analytical chemistry laboratories. The work described here aims at providing guidelines to achieve the best sequence coverage for the fragmentation of intact light and heavy chains generated from a simple reduction of intact antibodies using Orbitrap mass spectrometry. Three parameters were found crucial to this aim: the use of an electron-based activation technique, the multiplex selection of precursor ions of different charge states and the combination of replicates.

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“…There is an ongoing need for improved tools related to top-down data analysis. − Several popular programs exist in this space such as ProSight Lite which allows users to generate publication-quality sequence coverage maps, or TDValidator which serves as a one-stop shop for proteoform analysis. , MASH Explorer offers another comprehensive software suite for proteomics with additional focus on native MS analysis . TDFragMapper is another resource which aids the optimization of experimental parameters for top-down experiments . However, these programs have limitations pertaining to the types of information provided (such as sorting ions by type) and/or their accessibility.…”

Section: Introductionmentioning

confidence: 99%

“…15 TDFragMapper is another resource which aids the optimization of experimental parameters for top-down experiments. 16 However, these programs have limitations pertaining to the types of information provided (such as sorting ions by type) and/or their accessibility. Herein we present the Mass Spectrometry Tool for the Analysis of Fragment Ions, or MS-TAFI, as a free python-based software program for the analysis and visualization of TD-MS data.…”

Section: ■ Introductionmentioning

confidence: 99%

MS-TAFI: A Tool for the Analysis of Fragment Ions Generated from Intact Proteins

Juetten

Brodbelt

2022

J. Proteome Res.

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Tandem mass spectrometry (MS/MS) spectra of intact proteins can be difficult to interpret owing to the variety of fragment ion types and abundances. This information is crucial for maximizing the information derived from top-down mass spectrometry of proteins and protein complexes. MS-TAFI (Mass Spectrometry Tool for the Analysis of Fragment Ions) is a free Pythonbased program which offers a streamlined approach to the data analysis and visualization of deconvoluted MS/MS data of intact proteins. The application also contains tools for native mass spectrometry experiments with the ability to search for fragment ions that retain ligands (holo ions) as well as visualize the location of charge sites obtained from 193 nm ultraviolet photodissociation data. The source code and complete application for MS-TAFI is available for download at https:// github.com/kylejuetten.

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

Cited by 4 publications

References 7 publications

A multiparameter optimization in middle‐down analysis of monoclonal antibodies by LC–MS/MS

A multiparameter optimization in middle‐down analysis of monoclonal antibodies by LC–MS/MS

A multi-parameter optimization in middle-down analysis of monoclonal antibodies by LC-MS/MS

MS-TAFI: A Tool for the Analysis of Fragment Ions Generated from Intact Proteins

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