ProteoCombiner: integrating bottom-up with top-down proteomics data for improved proteoform assessment.

Autor:	Lima DB; Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS USR 2000, Paris, France., Dupré M; Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS USR 2000, Paris, France., Duchateau M; Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS USR 2000, Paris, France., Gianetto QG; Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS USR 2000, Paris, France.; Bioinformatics and Biostatistics HUB, Computational Biology Department, Institut Pasteur, CNRS USR 3756, Paris, France., Rey M; Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS USR 2000, Paris, France., Matondo M; Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS USR 2000, Paris, France., Chamot-Rooke J; Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS USR 2000, Paris, France.
Jazyk:	angličtina
Zdroj:	Bioinformatics (Oxford, England) [Bioinformatics] 2021 Aug 09; Vol. 37 (15), pp. 2206-2208.
DOI:	10.1093/bioinformatics/btaa958
Abstrakt:	Motivation: We present a high-performance software integrating shotgun with top-down proteomic data. The tool can deal with multiple experiments and search engines. Enable rapid and easy visualization, manual validation and comparison of the identified proteoform sequences including the post-translational modification characterization. Results: We demonstrate the effectiveness of our approach on a large-scale Escherichia coli dataset; ProteoCombiner unambiguously shortlisted proteoforms among those identified by the multiple search engines. Availability and Implementation: ProteoCombiner, a demonstration video and user tutorial are freely available at https://proteocombiner.pasteur.fr, for academic use; all data are thus available from the ProteomeXchange consortium (identifier PXD017618). Supplementary Information: Supplementary data are available at Bioinformatics online. (© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
Databáze:	MEDLINE
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