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Journal articles
Top-Down Garbage Collector: a tool for selecting high-quality top-down proteomics mass spectra
Diogo Lima
1
André Silva
2
Mathieu Dupré
1
Marlon Santos
2
Milan Clasen
2
Louise Kurt
2
Priscila Aquino
3
Valmir Barbosa
4
Paulo Carvalho
2, *
Julia Chamot-Rooke
1, *
*
Corresponding author
Paulo Carvalho 2
Correspondent author
Julia Chamot-Rooke 1
Correspondent author IdHAL : jchamot ORCID : https://orcid.org/0000-0002-9427-543X
1
UTechS MSBio - Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (Département Biologie structurale et Chimie
C2RT
25-28, rue du Docteur Roux
75724 Paris cedex 15 - France)
- Institut Pasteur [Paris] (25-28, rue du docteur Roux, 75724 Paris cedex 15 - France)
- INC - Institut de Chimie du CNRS (3 Rue Michel-Ange 75 016 Paris - France)
- CNRS - Centre National de la Recherche Scientifique : UAR2024 / USR2000 (France)
2
ICC - Fiocruz Paraná - Instituto Carlos Chagas / Carlos Chagas Institute [Curitiba, Brésil] (Rua Prof. Algacyr Munhoz Mader, 3775 - CIC 81350-010 Curitiba/PR, Brasil - Brazil)
- FIOCRUZ - Fundação Oswaldo Cruz (Av. Brasil, 4365 - Manguinhos, Rio de Janeiro - Brazil)
- RIIP - Réseau International des Instituts Pasteur (25, rue du Dr Roux 75724 Paris Cedex 15 - France)
3
ILMD - Instituto Leônidas e Maria Deane - Fiocruz Amazônia [Manaus, Brésil] (476 Teresina Street. Adrianópolis. Manaus - AM - Brazil)
- FIOCRUZ - Fundação Oswaldo Cruz (Av. Brasil, 4365 - Manguinhos, Rio de Janeiro - Brazil)
- RIIP - Réseau International des Instituts Pasteur (25, rue du Dr Roux 75724 Paris Cedex 15 - France)
4
UFRJ - Universidade Federal do Rio de Janeiro (Av. Pedro Calmon, 550 - Cidade Universitária, Rio de Janeiro - RJ, 21941-901 - Brazil)
Abstract : MOTIVATION:
We present the first tool for unbiased quality control of top-down proteomics datasets. Our tool can select high-quality top-down proteomics spectra, serve as a gateway for building top-down spectral libraries and, ultimately, improve identification rates.
RESULTS:
We demonstrate that a twofold rate increase for two E. coli top-down proteomics datasets may be achievable.
AVAILABILITY AND IMPLEMENTATION:
http://patternlabforproteomics.org/tdgc, freely available for academic use.
SUPPLEMENTARY INFORMATION:
Supplementary data are available at Bioinformatics online.
Document type :
Journal articles
Complete list of metadata
https://hal-pasteur.archives-ouvertes.fr/pasteur-02330759
Contributor : Virginie Portelette Connect in order to contact the contributor
Submitted on : Thursday, October 24, 2019 - 10:37:54 AM
Last modification on : Wednesday, January 19, 2022 - 1:44:01 PM
Contributor : Virginie Portelette Connect in order to contact the contributor
Submitted on : Thursday, October 24, 2019 - 10:37:54 AM
Last modification on : Wednesday, January 19, 2022 - 1:44:01 PM
Identifiers
- HAL Id : pasteur-02330759, version 1
- DOI : 10.1093/bioinformatics/btz085
- PUBMED : 30715205
Citation
Diogo Lima, André Silva, Mathieu Dupré, Marlon Santos, Milan Clasen, et al.. Top-Down Garbage Collector: a tool for selecting high-quality top-down proteomics mass spectra. Bioinformatics, Oxford University Press (OUP), 2019, 35 (18), pp.3489-3490. ⟨10.1093/bioinformatics/btz085⟩. ⟨pasteur-02330759⟩
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