Protein Complex Identification and quantitative complexome by CN-PAGE

Abstract The majority of cellular processes are carried out by protein complexes. Various size fractionation methods have previously been combined with mass spectrometry to identify protein complexes. However, most of these approaches lack the quantitative information which is required to understand...

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Autores principales:	Michal Gorka, Corné Swart, Beata Siemiatkowska, Silvia Martínez-Jaime, Aleksandra Skirycz, Sebastian Streb, Alexander Graf
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2019
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/90e3b2b6363e439396cfacd544d944b2
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spelling	oai:doaj.org-article:90e3b2b6363e439396cfacd544d944b22021-12-02T15:08:47ZProtein Complex Identification and quantitative complexome by CN-PAGE10.1038/s41598-019-47829-72045-2322https://doaj.org/article/90e3b2b6363e439396cfacd544d944b22019-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-019-47829-7https://doaj.org/toc/2045-2322Abstract The majority of cellular processes are carried out by protein complexes. Various size fractionation methods have previously been combined with mass spectrometry to identify protein complexes. However, most of these approaches lack the quantitative information which is required to understand how changes of protein complex abundance and composition affect metabolic fluxes. In this paper we present a proof of concept approach to quantitatively study the complexome in the model plant Arabidopsis thaliana at the end of the day (ED) and the end of the night (EN). We show that size-fractionation of native protein complexes by Clear-Native-PAGE (CN-PAGE), coupled with mass spectrometry can be used to establish abundance profiles along the molecular weight gradient. Furthermore, by deconvoluting complex protein abundance profiles, we were able to drastically improve the clustering of protein profiles. To identify putative interaction partners, and ultimately protein complexes, our approach calculates the Euclidian distance between protein profile pairs. Acceptable threshold values are based on a cut-off that is optimized by a receiver-operator characteristic (ROC) curve analysis. Our approach shows low technical variation and can easily be adapted to study in the complexome in any biological system.Michal GorkaCorné SwartBeata SiemiatkowskaSilvia Martínez-JaimeAleksandra SkiryczSebastian StrebAlexander GrafNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 9, Iss 1, Pp 1-14 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Michal Gorka Corné Swart Beata Siemiatkowska Silvia Martínez-Jaime Aleksandra Skirycz Sebastian Streb Alexander Graf Protein Complex Identification and quantitative complexome by CN-PAGE
description	Abstract The majority of cellular processes are carried out by protein complexes. Various size fractionation methods have previously been combined with mass spectrometry to identify protein complexes. However, most of these approaches lack the quantitative information which is required to understand how changes of protein complex abundance and composition affect metabolic fluxes. In this paper we present a proof of concept approach to quantitatively study the complexome in the model plant Arabidopsis thaliana at the end of the day (ED) and the end of the night (EN). We show that size-fractionation of native protein complexes by Clear-Native-PAGE (CN-PAGE), coupled with mass spectrometry can be used to establish abundance profiles along the molecular weight gradient. Furthermore, by deconvoluting complex protein abundance profiles, we were able to drastically improve the clustering of protein profiles. To identify putative interaction partners, and ultimately protein complexes, our approach calculates the Euclidian distance between protein profile pairs. Acceptable threshold values are based on a cut-off that is optimized by a receiver-operator characteristic (ROC) curve analysis. Our approach shows low technical variation and can easily be adapted to study in the complexome in any biological system.
format	article
author	Michal Gorka Corné Swart Beata Siemiatkowska Silvia Martínez-Jaime Aleksandra Skirycz Sebastian Streb Alexander Graf
author_facet	Michal Gorka Corné Swart Beata Siemiatkowska Silvia Martínez-Jaime Aleksandra Skirycz Sebastian Streb Alexander Graf
author_sort	Michal Gorka
title	Protein Complex Identification and quantitative complexome by CN-PAGE
title_short	Protein Complex Identification and quantitative complexome by CN-PAGE
title_full	Protein Complex Identification and quantitative complexome by CN-PAGE
title_fullStr	Protein Complex Identification and quantitative complexome by CN-PAGE
title_full_unstemmed	Protein Complex Identification and quantitative complexome by CN-PAGE
title_sort	protein complex identification and quantitative complexome by cn-page
publisher	Nature Portfolio
publishDate	2019
url	https://doaj.org/article/90e3b2b6363e439396cfacd544d944b2
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Protein Complex Identification and quantitative complexome by CN-PAGE

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