Automated peptide mapping and protein-topographical annotation of proteomics data

BACKGROUND: In quantitative proteomics, peptide mapping is a valuable approach to combine positional quantitative information with topographical and domain information of proteins. Quantitative proteomic analysis of cell surface shedding is an exemplary application area of this approach. RESULTS: We...

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Autores principales: Videm, Pavankumar, Gunasekaran, Deepika, Schröder, Bernd, Mayer, Bettina, Biniossek, Martin L, Schilling, Oliver
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071796/
https://www.ncbi.nlm.nih.gov/pubmed/24946880
http://dx.doi.org/10.1186/1471-2105-15-207
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author Videm, Pavankumar
Gunasekaran, Deepika
Schröder, Bernd
Mayer, Bettina
Biniossek, Martin L
Schilling, Oliver
author_facet Videm, Pavankumar
Gunasekaran, Deepika
Schröder, Bernd
Mayer, Bettina
Biniossek, Martin L
Schilling, Oliver
author_sort Videm, Pavankumar
collection PubMed
description BACKGROUND: In quantitative proteomics, peptide mapping is a valuable approach to combine positional quantitative information with topographical and domain information of proteins. Quantitative proteomic analysis of cell surface shedding is an exemplary application area of this approach. RESULTS: We developed ImproViser ( http://www.improviser.uni-freiburg.de) for fully automated peptide mapping of quantitative proteomics data in the protXML data. The tool generates sortable and graphically annotated output, which can be easily shared with further users. As an exemplary application, we show its usage in the proteomic analysis of regulated intramembrane proteolysis. CONCLUSION: ImproViser is the first tool to enable automated peptide mapping of the widely-used protXML format.
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spelling pubmed-40717962014-06-27 Automated peptide mapping and protein-topographical annotation of proteomics data Videm, Pavankumar Gunasekaran, Deepika Schröder, Bernd Mayer, Bettina Biniossek, Martin L Schilling, Oliver BMC Bioinformatics Software BACKGROUND: In quantitative proteomics, peptide mapping is a valuable approach to combine positional quantitative information with topographical and domain information of proteins. Quantitative proteomic analysis of cell surface shedding is an exemplary application area of this approach. RESULTS: We developed ImproViser ( http://www.improviser.uni-freiburg.de) for fully automated peptide mapping of quantitative proteomics data in the protXML data. The tool generates sortable and graphically annotated output, which can be easily shared with further users. As an exemplary application, we show its usage in the proteomic analysis of regulated intramembrane proteolysis. CONCLUSION: ImproViser is the first tool to enable automated peptide mapping of the widely-used protXML format. BioMed Central 2014-06-19 /pmc/articles/PMC4071796/ /pubmed/24946880 http://dx.doi.org/10.1186/1471-2105-15-207 Text en Copyright © 2014 Videm et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Videm, Pavankumar
Gunasekaran, Deepika
Schröder, Bernd
Mayer, Bettina
Biniossek, Martin L
Schilling, Oliver
Automated peptide mapping and protein-topographical annotation of proteomics data
title Automated peptide mapping and protein-topographical annotation of proteomics data
title_full Automated peptide mapping and protein-topographical annotation of proteomics data
title_fullStr Automated peptide mapping and protein-topographical annotation of proteomics data
title_full_unstemmed Automated peptide mapping and protein-topographical annotation of proteomics data
title_short Automated peptide mapping and protein-topographical annotation of proteomics data
title_sort automated peptide mapping and protein-topographical annotation of proteomics data
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071796/
https://www.ncbi.nlm.nih.gov/pubmed/24946880
http://dx.doi.org/10.1186/1471-2105-15-207
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