We thank G. Rosenberger, A. Beyer, B. Collins and S. Nikolaev for discussions. We thank L. Reiter, R. Bruderer and O. Rinner from Biognosys AG for sharing their thoughts about cell line proteome analysis from a commercial perspective. We thank H. Zhang and J. Chen from Johns Hopkins University, D. Pflieger and O. Filhol-Cochet from CEA Grenoble, M. Riwanto from University Hospital Zurich, U. Greber and M. Suomalainen from the University of Zurich, C. Arrieumerlou from the University of Basel (through InfectX), M. Beck and M.-T. Mackmull from the European Molecular Biology Laboratory, C. Jorgensen and J. Worboys from the Cancer Research UK Manchester Institute, M. Peter and C. Barnes from ETH Zurich, and A. Venkitaraman and C. Williams from the University of Cambridge for providing us their HeLa cells.

The work was supported by the SystemsX.ch project PhosphoNetX PPM (to R.A.), TargetInfectX (to C.D.), the Swiss National Science Foundation (grant 3100A0-688 107679 to R.A.), the European Research Council (ERC-20140AdG 670821 to R.A.), the JRC for Computational Biomedicine (which was partially funded by Bayer AG, to J.S.-R.), the Swiss National Science Foundation (grant 163180 to S.E.A.), the European Research Council (grants AdG 249968 to S.E.A. and 616441-DISEASEAVATARS to G.T.), the Umberto Veronesi Foundation (fellowship to P.-L.G.), the ERA-NET Neuron Program (P.-L.G.), Regione Lombardia (Ricerca Indipendente 2012 to G.T.) and the Italian Ministry of Health (Ricerca Corrente to G.T.) E.G.W. was supported by an NIH F32 Ruth Kirchstein Fellowship (F32GM119190).