PT  - JOURNAL ARTICLE
AU  - Edward L. Huttlin
AU  - Raphael J. Bruckner
AU  - Jose Navarrete-Perea
AU  - Joe R. Cannon
AU  - Kurt Baltier
AU  - Fana Gebreab
AU  - Melanie P. Gygi
AU  - Alexandra Thornock
AU  - Gabriela Zarraga
AU  - Stanley Tam
AU  - John Szpyt
AU  - Alexandra Panov
AU  - Hannah Parzen
AU  - Sipei Fu
AU  - Arvene Golbazi
AU  - Eila Maenpaa
AU  - Keegan Stricker
AU  - Sanjukta Guha Thakurta
AU  - Ramin Rad
AU  - Joshua Pan
AU  - David P. Nusinow
AU  - Joao A. Paulo
AU  - Devin K. Schweppe
AU  - Laura Pontano Vaites
AU  - J. Wade Harper
AU  - Steven P. Gygi
TI  - Dual Proteome-scale Networks Reveal Cell-specific Remodeling of the Human Interactome
AID  - 10.1101/2020.01.19.905109
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.01.19.905109
4099  - http://biorxiv.org/content/early/2020/01/19/2020.01.19.905109.short
4100  - http://biorxiv.org/content/early/2020/01/19/2020.01.19.905109.full
AB  - Thousands of interactions assemble proteins into modules that impart spatial and functional organization to the cellular proteome. Through affinity-purification mass spectrometry, we have created two proteome-scale, cell-line-specific interaction networks. The first, BioPlex 3.0, results from affinity purification of 10,128 human proteins – half the proteome – in 293T cells and includes 118,162 interactions among 14,586 proteins; the second results from 5,522 immunoprecipitations in HCT116 cells. These networks model the interactome at unprecedented scale, encoding protein function, localization, and complex membership. Their comparison validates thousands of interactions and reveals extensive customization of each network. While shared interactions reside in core complexes and involve essential proteins, cell-specific interactions bridge conserved complexes, likely ‘rewiring’ each cell’s interactome. Interactions are gained and lost in tandem among proteins of shared function as the proteome remodels to produce each cell’s phenotype. Viewable interactively online through BioPlexExplorer, these networks define principles of proteome organization and enable unknown protein characterization.