FLEXIQuant-LF to quantify protein modification extent in label-free proteomics data.

Autor:	Schlaffner CN; F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, United States.; Department of Neurology, Harvard Medical School, Boston, United States., Kahnert K; Department of Pathology, Boston Children's Hospital, Boston, United States.; Bioinformatics Unit (MF1), Robert Koch Institute, Berlin, Germany.; Department of Medical Biotechnology, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany., Muntel J; Department of Pathology, Boston Children's Hospital, Boston, United States.; Department of Pathology, Harvard Medical School, Boston, United States., Chauhan R; F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, United States., Renard BY; Bioinformatics Unit (MF1), Robert Koch Institute, Berlin, Germany.; Data Analytics and Computational Statistics, Hasso-Plattner-Institute, Faculty of Digital Engineering, University of Potsdam, Potsdam, Germany., Steen JA; F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, United States.; Department of Neurology, Harvard Medical School, Boston, United States., Steen H; Department of Pathology, Boston Children's Hospital, Boston, United States.; Department of Pathology, Harvard Medical School, Boston, United States.; Precision Vaccines Program, Boston Children's Hospital, Boston, United States.
Jazyk:	angličtina
Zdroj:	ELife [Elife] 2020 Dec 07; Vol. 9. Date of Electronic Publication: 2020 Dec 07.
DOI:	10.7554/eLife.58783
Abstrakt:	Improvements in LC-MS/MS methods and technology have enabled the identification of thousands of modified peptides in a single experiment. However, protein regulation by post-translational modifications (PTMs) is not binary, making methods to quantify the modification extent crucial to understanding the role of PTMs. Here, we introduce FLEXIQuant-LF, a software tool for large-scale identification of differentially modified peptides and quantification of their modification extent without knowledge of the types of modifications involved. We developed FLEXIQuant-LF using label-free quantification of unmodified peptides and robust linear regression to quantify the modification extent of peptides. As proof of concept, we applied FLEXIQuant-LF to data-independent-acquisition (DIA) data of the anaphase promoting complex/cyclosome (APC/C) during mitosis. The unbiased FLEXIQuant-LF approach to assess the modification extent in quantitative proteomics data provides a better understanding of the function and regulation of PTMs. The software is available at https://github.com/SteenOmicsLab/FLEXIQuantLF. Competing Interests: CS, KK, JM, RC, BR, JS, HS No competing interests declared (© 2020, Schlaffner et al.)
Databáze:	MEDLINE
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