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

Nat Methods. 2016 Oct;13(10):837-40. doi: 10.1038/nmeth.3967. Epub 2016 Aug 29.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Biomarkers / metabolism
  • Cells, Cultured
  • Embryonic Stem Cells / metabolism
  • Meta-Analysis as Topic*
  • Mice
  • Proteins / metabolism*
  • Proteomics / methods*
  • Proteomics / statistics & numerical data
  • Subcellular Fractions / metabolism*


  • Biomarkers
  • Proteins