Abstract
Complexome profiling is an emerging ‘omics’ approach that systematically interrogates the composition of protein complexes (the complexome) of a sample, by combining biochemical separation of native protein complexes with mass-spectrometry based quantitation proteomics. The resulting fractionation profiles hold comprehensive information on the abundance and composition of the complexome, and have a high potential for reuse by experimental and computational researchers. However, the lack of a central resource that provides access to these data, reported with adequate descriptions and an analysis tool, has limited their reuse. Therefore, we established the ComplexomE profiling DAta Resource (CEDAR, www3.cmbi.umcn.nl/cedar/), an openly accessible database for depositing and exploring mass spectrometry data from complexome profiling studies. Compatibility and reusability of the data is ensured by a standardized data and reporting format containing the “minimum information required for a complexome profiling experiment” (MIACE). The data can be accessed through a user-friendly web interface, as well as programmatically using the REST API portal. Additionally, all complexome profiles available on CEDAR can be inspected directly on the website with the profile viewer tool that allows the detection of correlated profiles and inference of potential complexes. In conclusion, CEDAR is a unique, growing and invaluable resource for the study of protein complex composition and dynamics across biological systems.
Highlights
The complete inventory of multi-protein assemblies present in a sample is referred to as its complexome
We developed MIACE with the goal to increase the value of the growing number of complexome profiling experiments being performed
The purpose of MIACE is to provide a complete description of all the information required for comprehen sively reporting a complexome profiling experiment, for which it refers to existing documentation where applicable
Summary
The complete inventory of multi-protein assemblies present in a sample is referred to as its complexome. A number of methods are used to natively separate pro tein complexes in complexome profiling, such as blue-native gel elec trophoresis [4,5,14,15,16,17,18,6,7,8,9,10,11,12,13], size exclusion chromatography [19,20,21,22] and sucrose gradient ultracentrifugation [18,23] The result of such an experiment, i.e. a complexome profile, contains a measure of abundance in every separated fraction for each detected protein. Alterna tively, these abundance profiles can be used to calculate various distance or similarity metrics between proteins, which can in turn be used to generate large scale protein-protein interaction networks [9,21,25,26,27]
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