CIG-P: Circular Interaction Graph for Proteomics.

Christopher K Hobbs,Herbert H Tsang,Michelle Leung,H Alexander Ebhardt

doi:10.1186/1471-2105-15-344

Christopher K Hobbs, Herbert H Tsang + Show 2 more

Open Access

https://doi.org/10.1186/1471-2105-15-344

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Journal: BMC bioinformatics	Publication Date: Oct 31, 2014
Citations: 13	License type: cc-by

Affiliation: Trinity Western University, ETH Zurich

Abstract

BackgroundA typical affinity purification coupled to mass spectrometry (AP-MS) experiment includes the purification of a target protein (bait) using an antibody and subsequent mass spectrometry analysis of all proteins co-purifying with the bait (aka prey proteins). Like any other systems biology approach, AP-MS experiments generate a lot of data and visualization has been challenging, especially when integrating AP-MS experiments with orthogonal datasets.ResultsWe present Circular Interaction Graph for Proteomics (CIG-P), which generates circular diagrams for visually appealing final representation of AP-MS data. Through a Java based GUI, the user inputs experimental and reference data as file in csv format. The resulting circular representation can be manipulated live within the GUI before exporting the diagram as vector graphic in pdf format. The strength of CIG-P is the ability to integrate orthogonal datasets with each other, e.g. affinity purification data of kinase PRPF4B in relation to the functional components of the spliceosome. Further, various AP-MS experiments can be compared to each other.ConclusionsCIG-P aids to present AP-MS data to a wider audience and we envision that the tool finds other applications too, e.g. kinase – substrate relationships as a function of perturbation. CIG-P is available under: http://sourceforge.net/projects/cig-p/Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2105-15-344) contains supplementary material, which is available to authorized users.

Highlights

A typical affinity purification coupled to mass spectrometry (AP-MS) experiment includes the purification of a target protein using an antibody and subsequent mass spectrometry analysis of all proteins co-purifying with the bait
We present Circular Interaction Graph for Proteomics (CIG-P), which generates circular diagrams for visually appealing final representation of AP-MS data
CIG-P aids to present AP-MS data to a wider audience and we envision that the tool finds other applications too, e.g. kinase – substrate relationships as a function of perturbation

Summary

Background

Proteomics using high mass accuracy mass spectrometers aims to characterize the proteome of a cell over space and time [1]. Following the enrichment of bait protein, bait-associated proteins will co-purify (termed: prey or interactors) and are identified by subsequent standard bottom-up proteomics approach using high mass accuracy mass spectrometry [3]. From the black section of SRPK1 (bait protein), colored arcs are drawn representing the high quality protein-protein interactions found in each AP-MS experiment. Implementation For generating circular diagrams, we developed an intuitive Java based graphical user interface termed CIG-P which uses three input files: an experiment file containing the actual AP-MS experiment, a reference file containing a dataset to which the experiment is compared to and lastly a RBG color scheme (see Additional files 1, 2, 3, 4, 5 for examples). More details on the organization of these files can be found in the (Additional file 2) User_Manual

Results

Conclusions

Results and Discussion