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PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data
Joint Authors
Labudde, Dirk
Schildbach, Stefan
Blumert, Conny
Horn, Friedemann
von Bergen, Martin
Kalkhof, Stefan
Source
Issue
Vol. 2016, Issue 2016 (31 Dec. 2016), pp.1-13, 13 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2016-02-07
Country of Publication
Egypt
No. of Pages
13
Main Subjects
Abstract EN
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.
American Psychological Association (APA)
Kalkhof, Stefan& Schildbach, Stefan& Blumert, Conny& Horn, Friedemann& von Bergen, Martin& Labudde, Dirk. 2016. PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data. BioMed Research International،Vol. 2016, no. 2016, pp.1-13.
https://search.emarefa.net/detail/BIM-1097184
Modern Language Association (MLA)
Kalkhof, Stefan…[et al.]. PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data. BioMed Research International No. 2016 (2016), pp.1-13.
https://search.emarefa.net/detail/BIM-1097184
American Medical Association (AMA)
Kalkhof, Stefan& Schildbach, Stefan& Blumert, Conny& Horn, Friedemann& von Bergen, Martin& Labudde, Dirk. PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data. BioMed Research International. 2016. Vol. 2016, no. 2016, pp.1-13.
https://search.emarefa.net/detail/BIM-1097184
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1097184