Increasing confidence in proteomic spectral deconvolution through mass defect.

Autor:	Clasen MA; Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz-Paraná 81310-020, Brazil., Kurt LU; Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz-Paraná 81310-020, Brazil., Santos MDM; Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz-Paraná 81310-020, Brazil., Lima DB; Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany., Liu F; Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany., Gozzo FC; Dalton Mass Spectrometry Laboratory, Unicamp, Campinas 13083-970, Brazil., Barbosa VC; Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, Rio de Janeiro 21941-972, Brazil., Carvalho PC; Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz-Paraná 81310-020, Brazil.
Jazyk:	angličtina
Zdroj:	Bioinformatics (Oxford, England) [Bioinformatics] 2022 Nov 15; Vol. 38 (22), pp. 5119-5120.
DOI:	10.1093/bioinformatics/btac638
Abstrakt:	Motivation: Confident deconvolution of proteomic spectra is critical for several applications such as de novo sequencing, cross-linking mass spectrometry and handling chimeric mass spectra. Results: In general, all deconvolution algorithms may eventually report mass peaks that are not compatible with the chemical formula of any peptide. We show how to remove these artifacts by considering their mass defects. We introduce Y.A.D.A. 3.0, a fast deconvolution algorithm that can remove peaks with unacceptable mass defects. Our approach is effective for polypeptides with less than 10 kDa, and its essence can be easily incorporated into any deconvolution algorithm. Availability and Implementation: Y.A.D.A. 3.0 is freely available for academic use at http://patternlabforproteomics.org/yada3. Supplementary Information: Supplementary information is available at Bioinformatics online. (© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
Databáze:	MEDLINE
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