Proteins interact with each other and organize themselves into macromolecular machines (ie. complexes) to carry out functions of the cell. Different cell-types and cellular conditions will affect the ultimate composition of protein complexes but we currently lack the identities of complexes present in different conditions. The stem.MAP attempts to address this lack of understanding by integrating co-fractionation mass spectrometry data to obtain a comprehensive view of protein complexes in mouse embryonic stem cells. In stem.MAP we integrated two size exclusion chromatography CF-MS datasets from Mallam et al. and one ion exchange chromatography CF-MS dataset from Cox et al. using a novel prior-based machine learning workflow to produce a stem cell specific complex map with ~4,000 complexes.

Contributers

  Kevin Drew (website)   Akshaya Rajaraman (website)

Funding

  NIH R35, NSF/BBSRC

Citation

• Coming soon.

References

• Anna L Mallam, Wisath Sae-Lee, Jeffrey M Schaub, Fan Tu, Anna Battenhouse, Yu Jin Jang, Jonghwan Kim, John B Wallingford, Ilya J Finkelstein, Edward M Marcotte, Kevin Drew Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes Cell Rep. 2019 Oct 29;29(5):1351–1368.e5. doi: 10.1016/j.celrep.2019.09.060
• Rachael M. Cox, Ophelia Papoulas, Shirlee Shril, Chanjae Lee, Tynan P. Gardner, Zoya T. Ansari, Anna M. Battenhouse, Muyoung Lee, Kevin Drew, Claire D. McWhite, David Yang, Janelle C. Leggere, Dannie Durand, Friedhelm Hildebrandt, John B. Wallingford, Edward M. Marcotte A protein interactome for the last eukaryotic common ancestor illuminates the biochemical basis of modern genetic diseases Cell Genom. 2026 Jun 10;6(6):101254. doi: 10.1016/j.xgen.2026.101254.

Contact

  proteincomplexmap (at) gmail.com