PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data
The functionality of most proteins is regulated by protein-protein interactions. Hence, the comprehensive characterization of the interactome is the next milestone on the path to understand the biochemistry of the cell. A powerful method to detect protein-protein interactions is a combination of coi...
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doaj-742f8e8080504b3abe71139d54322c5f2020-11-24T22:45:28ZengHindawi LimitedBioMed Research International2314-61332314-61412016-01-01201610.1155/2016/28919182891918PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry DataStefan Kalkhof0Stefan Schildbach1Conny Blumert2Friedemann Horn3Martin von Bergen4Dirk Labudde5Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, GermanyDepartment of Applied Computer Sciences & Biosciences, University of Applied Sciences Mittweida, 09648 Mittweida, GermanyInstitute of Clinical Immunology, Medical Faculty, University of Leipzig, 04103 Leipzig, GermanyInstitute of Clinical Immunology, Medical Faculty, University of Leipzig, 04103 Leipzig, GermanyDepartment of Proteomics, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, GermanyDepartment of Applied Computer Sciences & Biosciences, University of Applied Sciences Mittweida, 09648 Mittweida, GermanyThe functionality of most proteins is regulated by protein-protein interactions. Hence, the comprehensive characterization of the interactome is the next milestone on the path to understand the biochemistry of the cell. A powerful method to detect protein-protein interactions is a combination of coimmunoprecipitation or affinity purification with quantitative mass spectrometry. Nevertheless, both methods tend to precipitate a high number of background proteins due to nonspecific interactions. To address this challenge the software Protein-Protein-Interaction-Optimizer (PIPINO) was developed to perform an automated data analysis, to facilitate the selection of bona fide binding partners, and to compare the dynamic of interaction networks. In this study we investigated the STAT1 interaction network and its activation dependent dynamics. Stable isotope labeling by amino acids in cell culture (SILAC) was applied to analyze the STAT1 interactome after streptavidin pull-down of biotagged STAT1 from human embryonic kidney 293T cells with and without activation. Starting from more than 2,000 captured proteins 30 potential STAT1 interaction partners were extracted. Interestingly, more than 50% of these were already reported or predicted to bind STAT1. Furthermore, 16 proteins were found to affect the binding behavior depending on STAT1 phosphorylation such as STAT3 or the importin subunits alpha 1 and alpha 6.http://dx.doi.org/10.1155/2016/2891918 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Stefan Kalkhof Stefan Schildbach Conny Blumert Friedemann Horn Martin von Bergen Dirk Labudde |
spellingShingle |
Stefan Kalkhof Stefan Schildbach Conny Blumert Friedemann Horn Martin von Bergen Dirk Labudde PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data BioMed Research International |
author_facet |
Stefan Kalkhof Stefan Schildbach Conny Blumert Friedemann Horn Martin von Bergen Dirk Labudde |
author_sort |
Stefan Kalkhof |
title |
PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data |
title_short |
PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data |
title_full |
PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data |
title_fullStr |
PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data |
title_full_unstemmed |
PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data |
title_sort |
pipino: a software package to facilitate the identification of protein-protein interactions from affinity purification mass spectrometry data |
publisher |
Hindawi Limited |
series |
BioMed Research International |
issn |
2314-6133 2314-6141 |
publishDate |
2016-01-01 |
description |
The functionality of most proteins is regulated by protein-protein interactions. Hence, the comprehensive characterization of the interactome is the next milestone on the path to understand the biochemistry of the cell. A powerful method to detect protein-protein interactions is a combination of coimmunoprecipitation or affinity purification with quantitative mass spectrometry. Nevertheless, both methods tend to precipitate a high number of background proteins due to nonspecific interactions. To address this challenge the software Protein-Protein-Interaction-Optimizer (PIPINO) was developed to perform an automated data analysis, to facilitate the selection of bona fide binding partners, and to compare the dynamic of interaction networks. In this study we investigated the STAT1 interaction network and its activation dependent dynamics. Stable isotope labeling by amino acids in cell culture (SILAC) was applied to analyze the STAT1 interactome after streptavidin pull-down of biotagged STAT1 from human embryonic kidney 293T cells with and without activation. Starting from more than 2,000 captured proteins 30 potential STAT1 interaction partners were extracted. Interestingly, more than 50% of these were already reported or predicted to bind STAT1. Furthermore, 16 proteins were found to affect the binding behavior depending on STAT1 phosphorylation such as STAT3 or the importin subunits alpha 1 and alpha 6. |
url |
http://dx.doi.org/10.1155/2016/2891918 |
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