RESEARCH HIGHLIGHTS

PROTEOMICS The condition-dependent proteome

Absolute levels of the pro- ­efficiently without compromising amounts of 2,359 , or about 55% teome measured under 22 different condi- coverage. of the predicted E. coli proteome, across all tions represent a valuable resource. The researchers varied the experimental 22 conditions. They performed a number of Whereas the exists as a finite enti- conditions, including growing cells on mini- analyses, which included profiling 11 differ- ty, the proteome of an organism is a nebulous mal media while varying the energy source, ent post-translational modifications, look- thing. Even in a creature as tiny as E. coli, providing limited glucose while varying the ing at how levels of certain classes of protein the proteome is always changing. Using growth rate, providing excessive glucose change with the growth rate, evaluating the to take a snapshot of a while subjecting cells to different stresses, role of transcriptional regulation in allow- proteome tells one only what is happening and growing cells on complex media. They ing the to adapt to new conditions, and at that moment, under those experimental also profiled the proteome on different days understanding how proteins are distributed conditions. from the start of stationary phase. They among cellular compartments, in particular This is why a recent effort to quantita- developed optimized approaches for extract- the periplasm and cytoplasm, under differing tively profile the proteome of E. coli under ing membrane and ribosomal proteins, and conditions. 22 different experimental conditions they minimized sample prefractionation as All of the data are available via represents an intriguing and important much as possible for analysis by liquid chro- ProteomeXchange and should be of value resource. In this work, a team of research- matography coupled to high-resolution mass to systems biologists and E. coli researchers ers led by Matthias Heinemann of the spectrometry. To determine absolute concen- alike. University of Groningen and Alexander trations, they measured levels of 41 selected Allison Doerr Schmidt of the University of Basel devel- proteins with high accuracy and then used RESEARCH PAPERS oped a streamlined mass spectrometry– that information to calibrate the quantities of Schmidt, A. et al. The quantitative and condition- based platform that allowed all identified proteins. dependent Escherichia coli proteome. Nat. Biotechnol. them to amass a very large data set In total, the team measured the absolute doi:10.1038/nbt.3418 (7 December 2015). America, Inc. All rights reserved. America, Inc. © 201 6 Nature npg

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