MetaMass, a tool for meta-analysis of subcellular proteomics data

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MetaMass, a tool for meta-analysis of subcellular proteomics data

2016Nature America, Inc. All rights reserved.

2016Nature America, Inc. All rights reserved.

Fridtjof Lund-Johansen1,2, Daniel de la Rosa Carrillo1,3, Adi Mehta1,4, Krzysztof Sikorski1,2,

Marit Inngjerdingen1, Tomas Kalina5,

Kjetil Rysland6, Gustavo Antonio de Souza1, Andrew R M Bradbury7, Quentin Lecrevisse812 & Jan Stuchly5,12

We report a tool for the analysis of subcellular proteomics data, called MetaMass, based on the use of standardized lists of subcellular markers. We analyzed data from 11 studies using MetaMass, mapping the subcellular location of 5,970 proteins. Our analysis revealed large variations in the performance of subcellular fractionation protocols as well as systematic biases in protein annotation databases. The Excel and R versions of MetaMass should enhance transparency and reproducibility in subcellular proteomics.

The combination of subcellular fractionation and mass spec-trometry (MS) allows the spatial mapping of entire cellular proteomes14. While this opens the door to a systems-based approach to cell biology research, there is an urgent need for better standardization of experimental procedures and data analysis. Upon reviewing 90 recent publications in three proteomics journals, we determined that there is extensive variation in the methods used to prepare subcellular fractions and in the selection of organelle markers used to assess the partitioning of subcellular compartments (Supplementary Table 1). We also found that there is little overlap in the lists of proteins that are assigned a single sub-cellular location by Uniprot, the Gene Ontology Consortium (GO) and the Human Protein Atlas (HPA) (Supplementary Table 2 and Supplementary Fig. 1).

Reviews of subcellular proteomics studies suggest that the variation described above reflects the diversity of cellular proteomes and that fractionation protocols and organelle markers should be adapted to the cell type under investigation3,4. From this perspective, standardization seems impossible. However, we are unaware

of any attempts to perform meta-analysis of subcellular proteomics data, so the question of whether standardization is possible has remained unanswered. In fact, most proteomics researchers use western blotting rather than MS results to validate subcellular fractionation protocols (Supplementary Table 1). There can be little doubt that MS is more informative and, since MS data have a numerical format, it is feasible to use published data sets as reference.

Here, we developed tools for meta-analysis of subcellular proteomics data,...