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Open Access Software

Automated peptide mapping and protein-topographical annotation of proteomics data

Pavankumar Videm12, Deepika Gunasekaran1, Bernd Schröder3, Bettina Mayer1, Martin L Biniossek1 and Oliver Schilling145*

Author Affiliations

1 Institute of Molecular Medicine and Cell Research, University of Freiburg, D-79104 Freiburg, Germany

2 Present address: Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany

3 Biochemical Institute, Christian-Albrechts-University of Kiel, D-24118 Kiel, Germany

4 BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104 Freiburg, Germany

5 Stefan Meier Strasse 17, D-79104 Freiburg, Germany

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BMC Bioinformatics 2014, 15:207  doi:10.1186/1471-2105-15-207

Published: 19 June 2014

Abstract

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 webcite) 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.

Keywords:
Peptide mapping; Quantitative proteomics; Trans proteomic pipeline