Automated protein turnover calculations from 15N partial metabolic labeling LC/MS shotgun proteomics data.

Protein turnover is a well-controlled process in which polypeptides are constantly being degraded and subsequently replaced with newly synthesized copies. Extraction of composite spectral envelopes from complex LC/MS shotgun proteomics data can be a challenging task, due to the inherent complexity o...

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Autores principales:	David Lyon, Maria Angeles Castillejo, Christiana Staudinger, Wolfram Weckwerth, Stefanie Wienkoop, Volker Egelhofer
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d459744263114b5fa5bd3ac83fce802e
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spelling	oai:doaj.org-article:d459744263114b5fa5bd3ac83fce802e2021-11-18T08:23:14ZAutomated protein turnover calculations from 15N partial metabolic labeling LC/MS shotgun proteomics data.1932-620310.1371/journal.pone.0094692https://doaj.org/article/d459744263114b5fa5bd3ac83fce802e2014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24736476/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Protein turnover is a well-controlled process in which polypeptides are constantly being degraded and subsequently replaced with newly synthesized copies. Extraction of composite spectral envelopes from complex LC/MS shotgun proteomics data can be a challenging task, due to the inherent complexity of biological samples. With partial metabolic labeling experiments this complexity increases as a result of the emergence of additional isotopic peaks. Automated spectral extraction and subsequent protein turnover calculations enable the analysis of gigabytes of data within minutes, a prerequisite for systems biology high throughput studies. Here we present a fully automated method for protein turnover calculations from shotgun proteomics data. The approach enables the analysis of complex shotgun LC/MS 15N partial metabolic labeling experiments. Spectral envelopes of 1419 peptides can be extracted within an hour. The method quantifies turnover by calculating the Relative Isotope Abundance (RIA), which is defined as the ratio between the intensity sum of all heavy (15N) to the intensity sum of all light (14N) and heavy peaks. To facilitate this process, we have developed a computer program based on our method, which is freely available to download at http://promex.pph.univie.ac.at/protover.David LyonMaria Angeles CastillejoChristiana StaudingerWolfram WeckwerthStefanie WienkoopVolker EgelhoferPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 4, p e94692 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q David Lyon Maria Angeles Castillejo Christiana Staudinger Wolfram Weckwerth Stefanie Wienkoop Volker Egelhofer Automated protein turnover calculations from 15N partial metabolic labeling LC/MS shotgun proteomics data.
description	Protein turnover is a well-controlled process in which polypeptides are constantly being degraded and subsequently replaced with newly synthesized copies. Extraction of composite spectral envelopes from complex LC/MS shotgun proteomics data can be a challenging task, due to the inherent complexity of biological samples. With partial metabolic labeling experiments this complexity increases as a result of the emergence of additional isotopic peaks. Automated spectral extraction and subsequent protein turnover calculations enable the analysis of gigabytes of data within minutes, a prerequisite for systems biology high throughput studies. Here we present a fully automated method for protein turnover calculations from shotgun proteomics data. The approach enables the analysis of complex shotgun LC/MS 15N partial metabolic labeling experiments. Spectral envelopes of 1419 peptides can be extracted within an hour. The method quantifies turnover by calculating the Relative Isotope Abundance (RIA), which is defined as the ratio between the intensity sum of all heavy (15N) to the intensity sum of all light (14N) and heavy peaks. To facilitate this process, we have developed a computer program based on our method, which is freely available to download at http://promex.pph.univie.ac.at/protover.
format	article
author	David Lyon Maria Angeles Castillejo Christiana Staudinger Wolfram Weckwerth Stefanie Wienkoop Volker Egelhofer
author_facet	David Lyon Maria Angeles Castillejo Christiana Staudinger Wolfram Weckwerth Stefanie Wienkoop Volker Egelhofer
author_sort	David Lyon
title	Automated protein turnover calculations from 15N partial metabolic labeling LC/MS shotgun proteomics data.
title_short	Automated protein turnover calculations from 15N partial metabolic labeling LC/MS shotgun proteomics data.
title_full	Automated protein turnover calculations from 15N partial metabolic labeling LC/MS shotgun proteomics data.
title_fullStr	Automated protein turnover calculations from 15N partial metabolic labeling LC/MS shotgun proteomics data.
title_full_unstemmed	Automated protein turnover calculations from 15N partial metabolic labeling LC/MS shotgun proteomics data.
title_sort	automated protein turnover calculations from 15n partial metabolic labeling lc/ms shotgun proteomics data.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/d459744263114b5fa5bd3ac83fce802e
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Automated protein turnover calculations from 15N partial metabolic labeling LC/MS shotgun proteomics data.

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